# fidopt

> One open benchmark for biomedical image registration, segmentation and synthesis: 415 datasets, with the same test cases, the same scoring and the same rules for every method, classical or learned.

Use it to find the method that does best on a kind of problem (a leaderboard ranks one task, setting, pair of modalities and region), to read a method's scores on a dataset with what they are checked against, to find a test set with its licence and who made its annotations, or to run a method at the benchmark's settings with its KonfAI app. Every page below is plain HTML; https://fidopt.io/ is the same data as an interactive app. The results are a preview, generated on 2026-11-05 by fidopt 0.1.0: they can still change.

The fidopt package and its `fidopt score` and `fidopt submit` commands, the corpus on Hugging Face and the apps of its fideus-labs/fidopt-* repositories are private for now: there is no public way to submit results yet.

## The benchmark

- [Registration](https://fidopt.io/registration/): Its leaderboards, one per kind of problem: align a moving image onto a fixed one.
- [Segmentation](https://fidopt.io/segmentation/): Its leaderboards, one per kind of problem: outline the structures of an image.
- [Synthesis](https://fidopt.io/synthesis/): Its leaderboards, one per kind of problem: make the image of another modality from a source image.
- [The datasets](https://fidopt.io/datasets/): Every dataset of the corpus by task, kind of image, region and licence, and the public datasets looked at.
- [Methods](https://fidopt.io/methods/): Every method with its version, its licence and the number of datasets it is ranked on.
- [Submit a method](https://fidopt.io/submit/): The three ways onto the leaderboards (results, a KonfAI app, a container) and what a result is.
- [About](https://fidopt.io/about/): What the benchmark is for and who keeps it, the machines, and the protocol in full: the datasets, the scoring, how each method is run.

## Run a method

- [konfai-apps](https://pypi.org/project/konfai-apps/): The command line that runs a method's KonfAI app: `pip install konfai-apps`, then the `konfai-apps infer` command on the method's page.
- [TotalSegmentator (total), KonfAI app](https://huggingface.co/VBoussot/TotalSegmentator-KonfAI): A public KonfAI app, VBoussot/TotalSegmentator-KonfAI.
- [TotalSegmentator (total_mr), KonfAI app](https://huggingface.co/VBoussot/TotalSegmentator-KonfAI): A public KonfAI app, VBoussot/TotalSegmentator-KonfAI.
- [IMPACTSeg body, KonfAI app](https://huggingface.co/VBoussot/ImpactSeg): A public KonfAI app, VBoussot/ImpactSeg.
- [MRSegmentator, KonfAI app](https://huggingface.co/VBoussot/MRSegmentator-KonfAI): A public KonfAI app, VBoussot/MRSegmentator-KonfAI.
- [DentalSegmentator, KonfAI app](https://huggingface.co/VBoussot/DentalSegmentator-KonfAI): A public KonfAI app, VBoussot/DentalSegmentator-KonfAI.
- [TotalSynth MR to CT, KonfAI app](https://huggingface.co/VBoussot/ImpactSynth): A public KonfAI app, VBoussot/ImpactSynth.
- [TotalSynth CBCT to CT, KonfAI app](https://huggingface.co/VBoussot/ImpactSynth): A public KonfAI app, VBoussot/ImpactSynth.

## Leaderboards

- [Lung CT, same patient](https://fidopt.io/registration/lung-ct/): Registration leaderboard.
- [Abdomen CT, same patient](https://fidopt.io/registration/abdomen-ct-same/): Registration leaderboard.
- [Abdomen CT, inter-patient](https://fidopt.io/registration/abdomen-ct-inter/): Registration leaderboard.
- [Abdomen CT, inter-patient, automatic organ labels](https://fidopt.io/registration/abdomen-ct-inter-automatic/): Registration leaderboard.
- [Brain MR, inter-subject](https://fidopt.io/registration/brain-mr-inter/): Registration leaderboard.
- [Brain MR, same patient](https://fidopt.io/registration/brain-mr-same/): Registration leaderboard.
- [Two modalities, same patient](https://fidopt.io/registration/two-modalities/): Registration leaderboard.
- [Learn2Reg official validation pairs](https://fidopt.io/registration/learn2reg-validation/): Registration leaderboard.
- [Repeat scans, same patient](https://fidopt.io/registration/repeat-scans/): Registration leaderboard.
- [Repeat chest CT, same patient, tumour truth](https://fidopt.io/registration/repeat-scans-tumour/): Registration leaderboard.
- [Heart MR, same patient](https://fidopt.io/registration/heart-mr-same/): Registration leaderboard.
- [Heart SPECT, inter-patient](https://fidopt.io/registration/heart-spect-inter/): Registration leaderboard.
- [Heart CT, same animal, months apart](https://fidopt.io/registration/heart-ct-same/): Registration leaderboard.
- [Thorax and abdomen MR, breathing, same patient](https://fidopt.io/registration/body-mr-same/): Registration leaderboard.
- [Chest and body CT, inter-patient](https://fidopt.io/registration/body-ct-inter/): Registration leaderboard.
- [Head, neck and spine, inter-patient](https://fidopt.io/registration/head-spine-inter/): Registration leaderboard.
- [Knee MR, inter-patient](https://fidopt.io/registration/knee-mr-inter/): Registration leaderboard.
- [Hand MR, two poses, same patient](https://fidopt.io/registration/hand-mr-same/): Registration leaderboard.
- [Tumours under treatment, same patient](https://fidopt.io/registration/tumours-same/): Registration leaderboard.
- [Abdomen MR, inter-patient](https://fidopt.io/registration/abdomen-mr-inter/): Registration leaderboard.
- [Prostate MR, inter-patient](https://fidopt.io/registration/prostate-mr-inter/): Registration leaderboard.
- [Fluorescence microscopy, between animals](https://fidopt.io/registration/microscopy-inter/): Registration leaderboard.
- [Mouse micro-CT, same animal](https://fidopt.io/registration/mouse-microct-same/): Registration leaderboard.
- [Retina photographs (2D), same eye](https://fidopt.io/registration/retina-same/): Registration leaderboard.
- [Heart ultrasound (2D), same patient](https://fidopt.io/registration/heart-us-same/): Registration leaderboard.
- [Radiographs (2D), inter-patient](https://fidopt.io/registration/radiographs-inter/): Registration leaderboard.
- [Photographs of scenes (2D), two viewpoints or times](https://fidopt.io/registration/scenes-photo/): Registration leaderboard.
- [Photographs of scenes (2D), two viewpoints, points from depth and camera poses](https://fidopt.io/registration/scenes-photo-automatic/): Registration leaderboard.
- [Speckle images (2D), known sub-pixel displacement, ranked apart](https://fidopt.io/registration/speckle-synthetic/): Registration leaderboard.
- [Frames of a scene (2D), optical flow, ranked apart](https://fidopt.io/registration/scenes-flow/): Registration leaderboard.
- [Plants (2D), same plant over days](https://fidopt.io/registration/plants-same/): Registration leaderboard.
- [MR to CT, same patient (SynthRAD)](https://fidopt.io/registration/synthrad-mr-ct/): Registration leaderboard.
- [CBCT to CT, same patient (SynthRAD)](https://fidopt.io/registration/synthrad-cbct-ct/): Registration leaderboard.
- [Brain MR, inter-subject, automatic labels](https://fidopt.io/registration/brain-mr-inter-automatic/): Registration leaderboard.
- [Known deformation, two images of one session](https://fidopt.io/registration/known-warp/): Registration leaderboard.
- [Same patient, truth made by a program](https://fidopt.io/registration/same-patient-automatic/): Registration leaderboard.
- [Mouse CT to MR, ranked apart](https://fidopt.io/registration/mouse-ctmr-unverified/): Registration leaderboard.
- [Photographs of a planar scene (2D), ranked apart](https://fidopt.io/registration/planar-scenes-provider/): Registration leaderboard.
- [Abdomen CT, segmentation](https://fidopt.io/segmentation/seg-abdomen-ct/): Segmentation leaderboard.
- [Body CT, many structures, segmentation](https://fidopt.io/segmentation/seg-body-ct/): Segmentation leaderboard.
- [Abdomen MR, segmentation](https://fidopt.io/segmentation/seg-abdomen-mr/): Segmentation leaderboard.
- [Heart, segmentation](https://fidopt.io/segmentation/seg-heart/): Segmentation leaderboard.
- [Brain MR, segmentation](https://fidopt.io/segmentation/seg-brain-mr/): Segmentation leaderboard.
- [Chest CT, segmentation](https://fidopt.io/segmentation/seg-chest-ct/): Segmentation leaderboard.
- [Head and neck, segmentation](https://fidopt.io/segmentation/seg-head-neck/): Segmentation leaderboard.
- [Spine, bones and joints, segmentation](https://fidopt.io/segmentation/seg-spine-bones/): Segmentation leaderboard.
- [Prostate and pelvis, segmentation](https://fidopt.io/segmentation/seg-prostate-pelvis/): Segmentation leaderboard.
- [Lesions and tumours, segmentation](https://fidopt.io/segmentation/seg-lesions/): Segmentation leaderboard.
- [One lesion in a CT volume of interest, segmentation](https://fidopt.io/segmentation/seg-lesion-voi/): Segmentation leaderboard.
- [Vessels, segmentation](https://fidopt.io/segmentation/seg-vessels/): Segmentation leaderboard.
- [Cone-beam CT, ultrasound and mouse, segmentation](https://fidopt.io/segmentation/seg-other/): Segmentation leaderboard.
- [MR to CT, synthesis](https://fidopt.io/synthesis/syn-mr-ct/): Synthesis leaderboard.
- [CBCT to CT, synthesis](https://fidopt.io/synthesis/syn-cbct-ct/): Synthesis leaderboard.
- [MR to MR, another contrast, field strength or scanner, synthesis](https://fidopt.io/synthesis/syn-mr-mr/): Synthesis leaderboard.
- [MR to MR, one acquisition to the mean of its repetitions, synthesis](https://fidopt.io/synthesis/syn-mr-denoising/): Synthesis leaderboard.
- [Microscopy (2D), two modalities, known deformation](https://fidopt.io/registration/microscopy-known-warp/): Registration leaderboard.
- [CT to PET, synthesis](https://fidopt.io/synthesis/syn-ct-pet/): Synthesis leaderboard.
- [Histology serial sections (2D), same block](https://fidopt.io/registration/histology-same/): Registration leaderboard.
- [Body MR, many structures, segmentation](https://fidopt.io/segmentation/seg-body-mr/): Segmentation leaderboard.
- [CBCT to CT, values scaled per image, synthesis](https://fidopt.io/synthesis/syn-cbct-ct-scaled/): Synthesis leaderboard.
- [Light-sheet microscopy of whole mice, between animals](https://fidopt.io/registration/mouse-lightsheet-inter/): Registration leaderboard.
- [Abdomen CT, same patient, files without their voxel size](https://fidopt.io/registration/abdomen-ct-same-voxels/): Registration leaderboard.
- [Pelvis CT to CT and MR to CT, same patient](https://fidopt.io/registration/pelvis-same-few/): Registration leaderboard.
- [Optical to SAR (2D), same place](https://fidopt.io/registration/optical-sar-same/): Registration leaderboard.
- [PET to CT, synthesis](https://fidopt.io/synthesis/syn-pet-ct/): Synthesis leaderboard.
- [CT to CT, another reconstruction, dose or contrast phase, synthesis](https://fidopt.io/synthesis/syn-ct-ct/): Synthesis leaderboard.
- [MR to PET, synthesis](https://fidopt.io/synthesis/syn-mr-pet/): Synthesis leaderboard.
- [Mouse brain MR, between animals](https://fidopt.io/registration/mouse-brain-mr-inter/): Registration leaderboard.
- [Brain tumours, four MR sequences, segmentation](https://fidopt.io/segmentation/seg-brain-tumours-mr/): Segmentation leaderboard.
- [Several MR sequences to the contrast T1, synthesis](https://fidopt.io/synthesis/syn-mr-sequences/): Synthesis leaderboard.
- [Stroke lesion, DWI and ADC, segmentation](https://fidopt.io/segmentation/seg-stroke-dwi-adc/): Segmentation leaderboard.
- [Electron microscopy, organelles, segmentation](https://fidopt.io/segmentation/seg-electron-microscopy/): Segmentation leaderboard.
- [CBCT to CT of the lung, five patients, synthesis](https://fidopt.io/synthesis/syn-cbct-ct-few/): Synthesis leaderboard.
- [CT to sodium fluoride bone PET, nine patients, synthesis](https://fidopt.io/synthesis/syn-ct-pet-few/): Synthesis leaderboard.
- [Lung tumour and nodes on 4D CT, five patients, segmentation](https://fidopt.io/segmentation/seg-lung-tumour-few/): Segmentation leaderboard.
- [Multiple sclerosis lesions, files without their pixel size, segmentation](https://fidopt.io/segmentation/seg-ms-lesions-pixels/): Segmentation leaderboard.
- [Simulated CBCT to CT, synthesis](https://fidopt.io/synthesis/syn-cbct-ct-simulated/): Synthesis leaderboard.
- [Fluorescence microscopy, confocal to STED, synthesis](https://fidopt.io/synthesis/syn-fluorescence/): Synthesis leaderboard.
- [Uterus on MR of endometrial cancer, segmentation](https://fidopt.io/segmentation/seg-uterus-mr-mixed/): Segmentation leaderboard.
- [Lymph nodes on CT, the marked nodes only, segmentation](https://fidopt.io/segmentation/seg-lymph-nodes-marked/): Segmentation leaderboard.
- [Rib fractures on CT, loose regions about each break, segmentation](https://fidopt.io/segmentation/seg-rib-fractures-loose/): Segmentation leaderboard.
- [Brain metastasis on post-contrast MR, the resected lesion only, segmentation](https://fidopt.io/segmentation/seg-brain-mets-resected/): Segmentation leaderboard.
- [Body CT, repeated pairs of eight test patients](https://fidopt.io/registration/abdomen-ct-inter-repeated/): Registration leaderboard.
- [Fluorescence microscopy, repeated volumes of one worm](https://fidopt.io/registration/worm-same/): Registration leaderboard.
- [Motion-corrupted to still brain MR, corpus-aligned](https://fidopt.io/synthesis/syn-mr-motion/): Synthesis leaderboard.
- [Wide-field fluorescence to structured illumination](https://fidopt.io/synthesis/syn-widefield-sim/): Synthesis leaderboard.
- [Liver segmentation on CT without physical geometry](https://fidopt.io/segmentation/seg-liver-ct-voxels/): Segmentation leaderboard.
- [Left atrium on late gadolinium-enhanced MRI, segmentation](https://fidopt.io/segmentation/seg-left-atrium-lge/): Segmentation leaderboard.
- [Mouse embryo nuclei, fluorescence segmentation](https://fidopt.io/segmentation/seg-embryo-nuclei/): Segmentation leaderboard.
- [Rodent microvessels, multiphoton fluorescence segmentation](https://fidopt.io/segmentation/seg-microvessels-fluorescence/): Segmentation leaderboard.
- [Arterial liver MR, liver and hepatocellular carcinoma](https://fidopt.io/segmentation/seg-liver-hcc-mr-small/): Segmentation leaderboard.
- [Clinical pelvic bones, CTPelvic1K](https://fidopt.io/segmentation/seg-pelvic-clinic/): Segmentation leaderboard.
- [CLEM, known added deformation](https://fidopt.io/registration/clem-synthetic-small/): Registration leaderboard.
- [Marmoset STPT, propagated atlas regions](https://fidopt.io/registration/marmoset-stpt-automatic/): Registration leaderboard.
- [Endometriosis pelvic MRI, uterus and ovaries](https://fidopt.io/segmentation/seg-endometriosis-mr/): Segmentation leaderboard.
- [RibSeg v2, individual ribs](https://fidopt.io/segmentation/seg-ribs/): Segmentation leaderboard.
- [HNTS-MRG 2024, pretreatment tumour segmentation](https://fidopt.io/segmentation/seg-head-neck-tumour-mr/): Segmentation leaderboard.
- [Liver lesions, curated MRI](https://fidopt.io/segmentation/seg-liver-lesions-mr/): Segmentation leaderboard.
- [Drone to crewed aerial photographs](https://fidopt.io/registration/crasar-aerial/): Registration leaderboard.
- [Simulated 3D cardiac ultrasound](https://fidopt.io/registration/straus-synthetic-us/): Registration leaderboard.
- [UVDoc paper deformation](https://fidopt.io/registration/uvdoc-paper/): Registration leaderboard.
- [Cardiac cine MRI, model motion](https://fidopt.io/registration/cardiac-cine-simulation/): Registration leaderboard.
- [Serial EM, known in-plane deformation](https://fidopt.io/registration/serial-em-synthetic/): Registration leaderboard.
- [Prostate MR–TRUS, three annotated cases](https://fidopt.io/registration/prostate-mrus-three-cases/): Registration leaderboard.
- [CLEM-Reg cellular volumes](https://fidopt.io/registration/clemreg-cellular-volumes/): Registration leaderboard.
- [DeepLIIF IHC–DAPI, known deformation](https://fidopt.io/registration/deepliif-synthetic/): Registration leaderboard.
- [Lumbar vertebral bodies and discs, multiple scanners](https://fidopt.io/segmentation/seg-lumbar-multiscanner/): Segmentation leaderboard.
- [Ex vivo medial temporal lobe MRI, between donors](https://fidopt.io/registration/brain-mr-exvivo/): Registration leaderboard.
- [Head and neck MR during treatment, tumour centres](https://fidopt.io/registration/head-neck-mr-treatment-centres/): Registration leaderboard.
- [Ex-vivo temporal bone, CBCT segmentation](https://fidopt.io/segmentation/seg-temporal-bone-exvivo/): Segmentation leaderboard.
- [Marmoset MRI before and after fixation](https://fidopt.io/registration/marmoset-in-ex-vivo-mr/): Registration leaderboard.
- [Simulated thoracic CBCT, known motion](https://fidopt.io/registration/thorax-simulated-cbct-registration/): Registration leaderboard.
- [Simulated thoracic CBCT contours](https://fidopt.io/registration/thorax-simulated-cbct-segmentation/): Registration leaderboard.
- [Simulated CBCT to CT](https://fidopt.io/registration/thorax-simulated-cbct-synthesis/): Registration leaderboard.
- [MR-linac cine target motion](https://fidopt.io/registration/trackrad-target-motion/): Registration leaderboard.
- [MR-linac cine target segmentation](https://fidopt.io/segmentation/seg-trackrad-target/): Segmentation leaderboard.
- [ORION native ROIs, known warp](https://fidopt.io/registration/orion-roi-registration/): Registration leaderboard.
- [Attenuation CT to Galligas ventilation PET](https://fidopt.io/synthesis/syn-ct-ventilation-pet/): Synthesis leaderboard.
- [Histology, H&E to Hoechst on the same section, synthesis](https://fidopt.io/synthesis/syn-he-if/): Synthesis leaderboard.
- [Temporal bone CBCT, between donors](https://fidopt.io/registration/temporal-bone-cbct-inter/): Registration leaderboard.
- [Retinal vessels on fundus photographs, 2D segmentation](https://fidopt.io/segmentation/seg-retina-vessels-2d/): Segmentation leaderboard.
- [Lungs and heart on chest X-rays, 2D segmentation](https://fidopt.io/segmentation/seg-chest-xray-2d/): Segmentation leaderboard.
- [Prostate zones on T2 and ADC, segmentation](https://fidopt.io/segmentation/seg-prostate-zones-mr/): Segmentation leaderboard.
- [Prostate cancer on biparametric MR, segmentation](https://fidopt.io/segmentation/seg-prostate-cancer-bpmri/): Segmentation leaderboard.
- [Skin lesions on dermoscopy, 2D segmentation](https://fidopt.io/segmentation/seg-skin-lesions-2d/): Segmentation leaderboard.
- [Polyps on colonoscopy, 2D segmentation](https://fidopt.io/segmentation/seg-polyps-2d/): Segmentation leaderboard.
- [Fetal and obstetric ultrasound, 2D segmentation](https://fidopt.io/segmentation/seg-obstetric-us-2d/): Segmentation leaderboard.
- [Cervical lips on transvaginal ultrasound, nine examinations, 2D segmentation](https://fidopt.io/segmentation/seg-cervix-us-few/): Segmentation leaderboard.
- [Pelvic floor on transperineal ultrasound, 2D segmentation](https://fidopt.io/segmentation/seg-pelvic-floor-us-2d/): Segmentation leaderboard.
- [Lumbar multifidus on ultrasound, 2D segmentation](https://fidopt.io/segmentation/seg-multifidus-us-2d/): Segmentation leaderboard.
- [Ovarian tumours on contrast-enhanced ultrasound, 2D segmentation](https://fidopt.io/segmentation/seg-ovarian-ceus-2d/): Segmentation leaderboard.
- [Colon wall on transabdominal ultrasound, 2D segmentation](https://fidopt.io/segmentation/seg-colon-wall-us-2d/): Segmentation leaderboard.
- [Brachial plexus on neck ultrasound videos, 2D segmentation, ranked apart](https://fidopt.io/segmentation/seg-brachial-plexus-us-2d/): Segmentation leaderboard.
- [Breast tumours on ultrasound, 2D segmentation](https://fidopt.io/segmentation/seg-breast-tumour-us-2d/): Segmentation leaderboard.
- [Thyroid nodules on ultrasound, 2D segmentation](https://fidopt.io/segmentation/seg-thyroid-nodule-us-2d/): Segmentation leaderboard.
- [Cell nuclei on histology and fluorescence microscopy, 2D segmentation](https://fidopt.io/segmentation/seg-nuclei-2d/): Segmentation leaderboard.
- [Thyroid lobes on 3D ultrasound, segmentation](https://fidopt.io/segmentation/seg-thyroid-us/): Segmentation leaderboard.
- [Wide-field to structured illumination, 2D synthesis](https://fidopt.io/synthesis/syn-widefield-sim-2d/): Synthesis leaderboard.
- [Transmitted light to nucleus fluorescence, 2D synthesis](https://fidopt.io/synthesis/syn-transmitted-fluorescence-2d/): Synthesis leaderboard.
- [Transmitted light to fluorescence, 3D synthesis](https://fidopt.io/synthesis/syn-transmitted-fluorescence-3d/): Synthesis leaderboard.
- [Fluorescence microscopy, low to high exposure, three specimens, synthesis](https://fidopt.io/synthesis/syn-fluorescence-denoising-few/): Synthesis leaderboard.
- [Rigid registration, CT to ultrasound](https://fidopt.io/registration/rigid-ct-us/): Registration leaderboard.
- [Pediatric T1 MRI with automatic regional labels](https://fidopt.io/registration/adhd-pediatric-mr/): Registration leaderboard.
- [IXI atlas registration, automatic labels](https://fidopt.io/registration/ixi-atlas-automatic/): Registration leaderboard.
- [Colorectal TMA serial-section epithelium](https://fidopt.io/registration/colorectal-tma-automatic/): Registration leaderboard.
- [Light-sheet whole mouse brains, two channels, known warp (out of core)](https://fidopt.io/registration/lightsheet-mouse-brain-known-warp/): Registration leaderboard.
- [Electron microscopy, blocks of one animal each, segmentation](https://fidopt.io/segmentation/seg-em-blocks/): Segmentation leaderboard.
- [Cortical layers on histological sections (2D), one brain, segmentation](https://fidopt.io/segmentation/seg-histology-layers/): Segmentation leaderboard.
- [Cleared brains, light-sheet microscopy patches, segmentation](https://fidopt.io/segmentation/seg-lightsheet-patches/): Segmentation leaderboard.
- [Brain MR, inter-subject, simulated phantoms](https://fidopt.io/registration/brain-mr-inter-simulated/): Registration leaderboard.
- [Brain and head tissue classes on simulated MR, segmentation](https://fidopt.io/segmentation/seg-brain-mr-simulated/): Segmentation leaderboard.
- [Final infarct from acute diffusion and perfusion MR, segmentation](https://fidopt.io/segmentation/seg-stroke-outcome/): Segmentation leaderboard.
- [Diffusion MR to FLAIR of the same session, corpus-aligned, synthesis](https://fidopt.io/synthesis/syn-dwi-flair-registered/): Synthesis leaderboard.
- [Retinal layers on OCT B-scans, 2D segmentation](https://fidopt.io/segmentation/seg-retina-oct-2d/): Segmentation leaderboard.
- [Spatial transcriptomics, adjacent H&E sections (2D)](https://fidopt.io/registration/spatial-transcriptomics-sections/): Registration leaderboard.

## Methods

- [anatomix + ConvexAdam](https://fidopt.io/method/anatomix_convexadam/): ConvexAdam on anatomix and MIND-SSC features, the registration pipeline of the anatomix paper with its command-line defaults.
- [ANTs SyN](https://fidopt.io/method/ants/): SyN as the Learn2Reg 2024 organisers ran it for LUMIR: cross-correlation, from the identity, 100x70x50x20 iterations, single precision.
- [ANTs DenoiseImage](https://fidopt.io/method/ants_denoise/): ANTs' DenoiseImage, Manjón et al.'s adaptive non-local means for MR, at the command's defaults (Gaussian noise model, patch radius 1, search radius 2): no learnt weights.
- [BrainMorph](https://fidopt.io/method/brainmorph/): BrainMorph as the LUMIR organisers run it: 512 keypoints, the H model, thin-plate splines without regularisation; a keypoint network trained on 100,000 brain MR images.
- [Cellpose (cyto3)](https://fidopt.io/method/cellpose_cyto3/): Cellpose 3's generalist cyto3 model, trained on nine datasets among which the 2018 Data Science Bowl, run as the package's Cellpose class runs it at its defaults (grey, diameter 30), every mask one nucleus.
- [ConvexAdam (MIND)](https://fidopt.io/method/convexadam_mind/): convex_adam_MIND with the repository's defaults: MIND-SSC features, a coupled-convex coarse search, then Adam instance optimisation.
- [corrField](https://fidopt.io/method/corrfield/): corrfield.py with its defaults, on the authors' 1 mm grid or coarser: Foerstner keypoints inside the fixed image's lung mask, MIND-SSC, discrete matching, thin-plate splines.
- [CT-FM whole-body segmentation](https://fidopt.io/method/ctfm_wholebody/): CT-FM's whole-body model, a SegResNet pretrained by self-supervision on 148,000 CTs and fine-tuned on TotalSegmentator's training split: TotalSegmentator v2's 117 structures of a CT at its own resolution, run as its model card's notebook runs it.
- [deeds](https://fidopt.io/method/deeds/): deedsBCV with its defaults (MIND-SSC, discrete optimisation), from the corpus's rigidly aligned pair, on an isotropic grid as its README asks for thick slices.
- [Demons](https://fidopt.io/method/demons/): ITK's fast symmetric forces Demons as SimpleITK's Demons notebook runs it: 20 iterations, field smoothing 2, pyramid 4, 2, 1; on MR the moving histogram is first matched to the fixed one, as SimpleITK's Demons examples do.
- [DFCAN](https://fidopt.io/method/dfcan/): DFCAN, the Fourier channel attention network of the BioSR paper, with its authors' single-image models (wide field to linear SIM, one model a structure), run as their predict.py runs it.
- [DIPY non-local means](https://fidopt.io/method/dipy_nlmeans/): DIPY's blockwise non-local means with a Rician noise model, the noise's level estimated from the image by estimate_sigma, both at their defaults: no learnt weights.
- [elastix (B-spline)](https://fidopt.io/method/elastix_bspline/): elastix's own default B-spline parameter map (mutual information with a bending-energy penalty, four resolutions, 256 iterations, a 10 mm grid), run by IMPACT-Reg's elastix engine with the IMPACT metric unused: a preset of that engine, not elastix's own executable.
- [FastSurferVINN](https://fidopt.io/method/fastsurfer/): FastSurferVINN, three voxel-size independent 2D networks (axial, coronal, sagittal) whose views are aggregated: 95 structures of a T1-weighted brain, FreeSurfer's aseg and the 62 DKT cortical regions, run as its authors' run_fastsurfer.sh --seg_only runs it.
- [FCBFormer](https://fidopt.io/method/fcbformer/): FCBFormer, a PVTv2 transformer branch fused with a fully convolutional branch, with its authors' Kvasir-SEG model, run as their predict.py runs it: 352 x 352, the logits kept above 0.
- [FireANTs (tutorial settings)](https://fidopt.io/method/fireants/): The FireANTs library used alone as its first tutorial does: greedy deformable registration on local cross-correlation, from the aligned pair (the tutorial's affine stage left out, as for every method). Kept for the comparison of costs with IMPACT-Reg's FireANTs engine.
- [Gaussian blur](https://fidopt.io/method/gaussian_blur/): SimpleITK's recursive Gaussian smoothing at its default standard deviation, 1 mm along every axis: the simplest denoiser, no learnt weights.
- [greedy](https://fidopt.io/method/greedy/): greedy's deformable Quick Start command as first written (2019): NCC on a 2x2x2 window, 100x50x10 iterations, default smoothing; one intensity space, as its reference advises (NMI does not work very well for deformable registration).
- [InstanSeg](https://fidopt.io/method/instanseg/): InstanSeg's released nuclei models, brightfield (trained on TNBC, LyNSeC, NuInsSeg, IHC TMA and CoNSeP) or fluorescence (CPDMI 2023) as the image calls for, run as the package's README runs them, every nucleus one label.
- [KonfAI segmentation app](https://fidopt.io/method/konfai_segmentation/): A KonfAI segmentation app run through konfai-apps: the variant names an app of fideus-labs/fidopt-segmentation, or one of Valentin Boussot's apps where it lives; the app writes its own labels, matched with the dataset's structures by name.
- [KonfAI synthesis app](https://fidopt.io/method/konfai_synthesis/): A KonfAI synthesis app run through konfai-apps: the variant names an app of fideus-labs/fidopt-synthesis, or one of Valentin Boussot's apps where it lives; the app writes the image of the target modality on the image's grid.
- [lungmask](https://fidopt.io/method/lungmask/): lungmask's U-Net(R231), trained on 231 routine CTs of varied disease, the right and left lungs slice by slice, run as its authors' command line runs it.
- [Little W-Net](https://fidopt.io/method/lwnet/): Little W-Net, a small W-shaped network for retinal vessels, with its authors' DRIVE model, run by their predict_one_image.py: test-time flips, the threshold 0.42 they chose on DRIVE.
- [Medical SAM3](https://fidopt.io/method/medical_sam3/): SAM 3 fine-tuned on 33 medical datasets, its authors' 2D model prompted by text alone, no box or point: the structure the authors' prompt names, the mask of highest score above 0.1, as their evaluation script runs it.
- [MONAI BraTS SegResNet](https://fidopt.io/method/monai_brats/): MONAI's brats_mri_segmentation bundle, a SegResNet trained on BraTS 2018: the tumour core, whole tumour and enhancing tumour of a glioma from T1, T1c, T2 and FLAIR, as BraTS labels, run as the bundle's inference.json runs it.
- [MONAI wholeBody CT](https://fidopt.io/method/monai_wholebody/): MONAI's wholeBody_ct_segmentation bundle, a SegResNet trained on the TotalSegmentator dataset at 1.5 mm: TotalSegmentator v1's 104 structures of a CT, run as the bundle's inference.json runs it.
- [multiGradICON](https://fidopt.io/method/multigradicon/): unigradicon-register --model multigradicon with its defaults: the network's prediction, then 50 steps of instance optimisation on LNCC.
- [multiGradICON (lung masks)](https://fidopt.io/method/multigradicon_lungmask/): multiGradICON with its authors' lung protocol: each image multiplied by its lung mask. The field means nothing outside the lungs.
- [NiftyReg](https://fidopt.io/method/niftyreg/): reg_f3d with its defaults (cubic B-spline, NMI), from the corpus's rigidly aligned pair.
- [nnsyn](https://fidopt.io/method/nnsyn/): nnsyn, CSIRO AEHRC's nnU-Net ResEnc-L that regresses the CT (team KoalAI, first in SynthRAD2025's MR-to-CT task), with its authors' released SynthRAD2025 models, one per source modality and region, run as their challenge docker runs them on the one fold they published.
- [Otsu nuclei](https://fidopt.io/method/otsu_nuclei/): A classical baseline with no learnt weights: Otsu's threshold with scikit-image: the nuclei above it on a stained section's haematoxylin (colour deconvolution), or on the side of it that holds fewer pixels on a grey image; small holes and specks removed.
- [StarDist (H&E)](https://fidopt.io/method/stardist_he/): StarDist's pretrained 2D_versatile_he, nuclei as star-convex polygons, trained on MoNuSeg 2018 and TNBC, run as the README runs a pretrained model, every nucleus one label.
- [SynthMorph](https://fidopt.io/method/synthmorph/): SynthMorph, networks trained only on synthetic images drawn from brain label maps, so that one model registers brain MR of any contrast and resolution without preprocessing: joint affine and deformable registration, run as its authors' mri_synthmorph register runs it.
- [SynthSeg 1.0](https://fidopt.io/method/synthseg/): SynthSeg 1.0, a U-Net trained only on synthetic scans drawn from brain label maps, so that one model reads any MR contrast and resolution: 32 brain structures, run as its authors' SynthSeg_predict.py --v1 runs it.
- [SynthSR](https://fidopt.io/method/synthsr/): SynthSR 1.0, a U-Net trained on scans synthesised from brain label maps to turn a brain MR of any contrast, orientation and resolution into a 1 mm MPRAGE-like T1, run as its authors' predict_command_line.py runs it; brought back onto the input's grid and scaled onto the input's intensities.
- [TorchXRayVision PSPNet](https://fidopt.io/method/txv_pspnet/): TorchXRayVision's chest radiograph anatomy model, a PSPNet whose training images were not released: 14 structures, lungs and heart among them, from a frontal radiograph, run as the authors' segmentation notebook runs it.
- [uniGradICON](https://fidopt.io/method/unigradicon/): unigradicon-register with its defaults: the network's prediction, then 50 steps of instance optimisation on LNCC.
- [uniGradICON (lung masks)](https://fidopt.io/method/unigradicon_lungmask/): uniGradICON with its authors' lung protocol: each image multiplied by its lung mask. The field means nothing outside the lungs.
- [vismatch matchers](https://fidopt.io/method/vismatch/): 2D feature matchers run by vismatch, each with its authors' code and weights, the homography from the fixed image to the moving one fitted by OpenCV's MAGSAC: the variant names the matcher.
- [VM-UNet](https://fidopt.io/method/vmunet/): VM-UNet, a U-shaped network of Vision Mamba blocks, with its authors' ISIC 2018 checkpoint, run as their test loop runs it: normalised with their ISIC 2018 statistics, resized to 256 x 256, the sigmoid kept above 0.5.
- [warpfield](https://fidopt.io/method/warpfield/): The warpfield library with its default recipe's two deformable levels: FFT block matching of 2D projections on the GPU, from the aligned pair (the recipe's translation and affine levels left out, as for every method). The moving image is brought onto the fixed grid; each image is shifted to start at zero, the recipe's background clipping being made for microscopy.

## Datasets

- [ACDC](https://fidopt.io/dataset/ACDC/): Cine MR short-axis stack of one patient's heart at end diastole (fixed) and end systole (moving), both ventricular cavities and the myocardium drawn at both phases (ACDC, the MICCAI 2017 Automated Cardiac Diagnosis Challenge).
- [ACDC, cardiac cine MR](https://fidopt.io/dataset/ACDC_Seg/): Short-axis cine MR stack of one patient's heart at end diastole or end systole, with the right ventricular cavity, the myocardium and the left ventricular cavity drawn by hand (ACDC, MICCAI 2017).
- [ACOUSLIC-AI, the fetal abdomen on blind-sweep ultrasound](https://fidopt.io/dataset/ACOUSLIC/): One frame of six blind ultrasound sweeps over a pregnant woman's abdomen, made by a novice with a low-cost probe, with the fetal abdomen drawn as an ellipse by a trained reader: one subject of ACOUSLIC-AI's training set (Sierra Leone).
- [ACRIN 6668, CT to FDG-PET](https://fidopt.io/dataset/ACRIN6668_CTPET_Syn/): CT and FDG-PET from one PET/CT session of a patient with non-small-cell lung cancer in the ACRIN 6668 trial: the CT is the source, the PET in body-weight SUV on its native grid the target.
- [Pediatric T1 MRI with and without previous ADHD diagnosis](https://fidopt.io/dataset/ADHDChildrenMR/): T1 MR of the brains of two different children from OpenNeuro ds002424, with FastSurfer anatomical labels on both; the test children have a parent-reported previous ADHD diagnosis.
- [AFIDs](https://fidopt.io/dataset/AFIDs/): Whole-head brain T1 MR of two subjects of one image set, SNSX at 7 T or LHSCPD at 1.5 T, each with the 32 anatomical fiducials of the AFIDs protocol.
- [Mouse whole-body light-sheet (AIMOS)](https://fidopt.io/dataset/AIMOSLightSheet/): Light-sheet fluorescence scans of two cleared mice, cropped from the head to the hips, showing the tissue's auto-fluorescence, with six organs drawn by hand on both (AIMOS, Schoppe et al. 2020), paired by us.
- [AIND SmartSPIM whole mouse brains, two channels](https://fidopt.io/dataset/AINDSmartSPIM/): Two channels of one cleared whole mouse brain, imaged by SmartSPIM light-sheet and fused on one grid: 488 nm fixed, 639 nm moving and deformed by a known smooth transform (Allen Institute for Neural Dynamics).
- [AMOS CT/CT](https://fidopt.io/dataset/AMOS_CTCT/): Abdominal CT scans of two patients from two scanners, paired by us from AMOS 2022, with 15 organs labelled on both.
- [AMOS CT, abdominal organs](https://fidopt.io/dataset/AMOS_CTCT_Seg/): Abdominal CT of one patient from the CT part of AMOS 2022, with the AMOS annotations of 15 organs.
- [AMOS MR/MR](https://fidopt.io/dataset/AMOS_MRMR/): Abdominal MR scans of two patients, paired by us from AMOS 2022, with 12 or 13 organs labelled on both.
- [AMOS MR, abdominal organs](https://fidopt.io/dataset/AMOS_MRMR_Seg/): Abdominal MR of one patient with the AMOS annotations of its organs (AMOS 2022, MR part).
- [ATM22](https://fidopt.io/dataset/ATM22/): One chest CT without contrast from the Shanghai Chest Hospital, from healthy people to patients with severe lung disease, with the airway tree labelled down to the small bronchi (ATM'22 challenge, first training batch).
- [Aariz cephalograms](https://fidopt.io/dataset/AarizCeph/): Two lateral cephalograms, 2D radiographs of the head seen from the side, of two orthodontic patients from one device, with 29 landmarks of bone, teeth and soft tissue placed by orthodontists (Aariz, test split).
- [Abdominal-DIR-QA](https://fidopt.io/dataset/AbdomenDIRQA/): Contrast-enhanced CT of the abdomen of one patient at two dates (Abdominal-DIR-QA).
- [Adrenal-ACC-Ki67-Seg](https://fidopt.io/dataset/AdrenalACC/): Contrast-enhanced abdominal CT of a patient with an adrenocortical carcinoma before its resection, the tumour outlined semi-automatically and refined by hand by a radiologist (Adrenal-ACC-Ki67-Seg, MD Anderson Cancer Center, TCIA).
- [AeroPath](https://fidopt.io/dataset/AeroPath/): A contrast-enhanced chest CT angiography of a patient examined for lung cancer, most with disease that deforms the airways, with the airway tree labelled (AeroPath).
- [Allen label-free prediction, bright field to lamin B1 fluorescence, 3D](https://fidopt.io/dataset/AllenLabelFree_Syn/): One field of view of live human induced pluripotent stem cells in 3D: the transmitted-light bright-field stack (source) and the fluorescence stack of their mEGFP-tagged lamin B1, the nuclear envelope (target), of one acquisition (Allen Institute for Cell Science, label-free prediction data).
- [Allen hiPSC single-cell image dataset, bright field to DNA, 3D](https://fidopt.io/dataset/AllenWTC11_Syn/): One field of view of live gene-edited WTC-11 human induced pluripotent stem cells in 3D: the transmitted-light bright-field stack (source) and the Hoechst-stained DNA stack (target) of one acquisition (Allen Institute for Cell Science, hiPSC single-cell image dataset).
- [Lausanne TOF-MRA aneurysms](https://fidopt.io/dataset/AneurysmTOF/): Time-of-flight MR angiography of the head of a patient with unruptured intracranial aneurysms, each traced voxel by voxel by a radiologist and checked by a senior neuroradiologist (Lausanne TOF-MRA Aneurysm Cohort, OpenNeuro ds003949).
- [AVT aortic vessel tree](https://fidopt.io/dataset/AorticTreeCTA/): CT, usually an angiography, from the neck to the groin of one patient, the aorta and its branches labelled as one structure (AVT aortic vessel tree, the training set of the SEG.A. 2023 challenge).
- [FDG-PET-CT-Lesions (autoPET)](https://fidopt.io/dataset/AutoPETCT/): Whole-body CT (fixed) and FDG-PET (moving) of one PET/CT session of a patient with melanoma, lymphoma or lung cancer or of a negative control, the PET deformed by a known smooth transform (autoPET).
- [FDG-PET-CT-Lesions (autoPET), CT to PET](https://fidopt.io/dataset/AutoPET_CTPET_Syn/): Contrast-enhanced CT (source) and FDG-PET in SUV (target) from one whole-body PET/CT session, neck down, of a patient with melanoma, lymphoma or lung cancer, or a negative control, on the PET's grid (FDG-PET-CT-Lesions, autoPET).
- [FDG-PET-CT-Lesions (autoPET), PET lesions](https://fidopt.io/dataset/AutoPET_Seg/): Whole-body FDG-PET in SUV, from the neck down, of a patient with melanoma, lymphoma or non-small cell lung cancer, every FDG-avid lesion judged malignant drawn by an experienced radiologist (FDG-PET-CT-Lesions, the autoPET data).
- [PSMA-PET-CT-Lesions (autoPET III and IV)](https://fidopt.io/dataset/AutoPSMA/): Whole-body CT (fixed) and PSMA-PET (moving) of one PET/CT session of a man with suspected or diagnosed prostate cancer, the PET deformed by a known smooth transform (PSMA-PET-CT-Lesions, autoPET III and IV).
- [PSMA-PET-CT-Lesions (autoPET III and IV), CT to PET](https://fidopt.io/dataset/AutoPSMA_CTPET_Syn/): One whole-body PSMA-PET/CT session of a man with suspected or diagnosed prostate cancer: the diagnostic CT brought onto the PET's grid (source) and the PET in SUV (target) (PSMA-PET-CT-Lesions, autoPET III and IV).
- [BITE](https://fidopt.io/dataset/BITE/): Intra-operative 3D ultrasound before resection (fixed) and pre-operative T1-weighted MR with gadolinium (moving) of one patient with a brain tumour (MNI BITE database, group 2).
- [Baby Open Brains (BOBs)](https://fidopt.io/dataset/BOBs/): Brain T2w MR of one infant at two visits 2 to 6 months apart, between 1 and 9 months of age (Baby Open Brains, from the Baby Connectome Project).
- [Baby Open Brains, 31 structures](https://fidopt.io/dataset/BOBs_Seg/): Brain MR of one infant with the dataset's segmentation of 31 structures (Baby Open Brains).
- [BUS-BRA, breast ultrasound tumours outlined by hand](https://fidopt.io/dataset/BUSBRA/): A 2D B-mode breast ultrasound image of a woman's biopsy-proven tumour, benign or malignant, outlined by hand by a senior ultrasonographer: one image a patient of BUS-BRA's 1,064 (National Cancer Institute, Rio de Janeiro).
- [BUSI, breast ultrasound lesions outlined by hand](https://fidopt.io/dataset/BUSI/): A 2D B-mode breast ultrasound image of a woman's benign or malignant lesion, outlined freehand and reviewed by radiologists: one of BUSI's 780 images (Baheya Hospital, Cairo, Al-Dhabyani et al. 2020), each group of copies counted once.
- [BUU-LSPINE lumbar radiographs](https://fidopt.io/dataset/BUULSpine/): Lateral radiographs of the lumbar spine of two patients of Burapha University Hospital, with the anterior and posterior corners of the endplates of L1 to L5 and of the top of S1 placed by physicians on each (BUU-LSPINE).
- [BigBrain cortical layers, manual annotations](https://fidopt.io/dataset/BigBrainLayers/): A coronal histological section of the BigBrain, a cell-body-stained human brain at 20 µm, cut about the strips of cortex on which its six layers were drawn by hand.
- [BioSR wide-field to linear SIM, F-actin, 2D](https://fidopt.io/dataset/BioSR_Actin_Syn/): One F-actin cell of BioSR, in 2D: the wide-field image at the lowest signal level, the mean of nine raw SIM images, as source, and the linear SIM image of the same field as target.
- [BioSR wide-field to linear SIM, clathrin-coated pits, 2D](https://fidopt.io/dataset/BioSR_CCP_Syn/): A 2D wide-field fluorescence image of clathrin-coated pits in one cell at BioSR's lowest signal level as source, and the linear SIM image of the same field as target (BioSR, Qiao et al., Nature Methods 2021).
- [BioSR wide-field to linear SIM, endoplasmic reticulum, 2D](https://fidopt.io/dataset/BioSR_ER_Syn/): One cell's endoplasmic reticulum in 2D: the wide-field image at the lowest signal level, the mean of nine raw SIM images, with the linear SIM image of the same field as target (BioSR).
- [BioSR wide-field to linear SIM, microtubules, 2D](https://fidopt.io/dataset/BioSR_MT_Syn/): One cell of BioSR's microtubules (Qiao et al., Nature Methods 2021): a 2D wide-field image at the lowest signal level, the mean of nine raw SIM images, with the linear SIM image as target.
- [BioTISR wide-field to 3D-SIM, live COS-7 cells](https://fidopt.io/dataset/BioTISR_Syn/): The wide-field fluorescence volume of one live COS-7 cell region at low excitation, its first time point, with the provider's higher-excitation 3D-SIM reconstruction as target: F-actin, microtubules or mitochondria.
- [Human Bony Labyrinth](https://fidopt.io/dataset/BonyLabyrinth/): Clinical CT (fixed) and micro-CT (moving) of one human temporal bone specimen, cropped around the inner ear, the micro-CT deformed by a known smooth transform (Human Bony Labyrinth).
- [MR enterography bowel segments](https://fidopt.io/dataset/BowelSegmentsMR/): Coronal T2-weighted MR enterography at 3 T of one patient with Crohn's disease, the bowel drawn in ten segments from the stomach to the rectum (Zhong et al., Sci Data 2025).
- [BraTS 2021 adult glioma](https://fidopt.io/dataset/BraTS2021/): Pre-treatment brain MR of an adult with a glioma, T1, T1Gd, T2 and FLAIR as one four-channel image, with the necrotic core, oedema and enhancing tumour labelled (RSNA-ASNR-MICCAI BraTS 2021 training set, TCIA).
- [BraTS 2021 adult glioma, T1, T2 and FLAIR to T1Gd](https://fidopt.io/dataset/BraTS2021_Syn/): One pre-operative brain MR of an adult with a glioma, on the BraTS pipeline's skull-stripped 1 mm SRI24 grid: T1, T2 and FLAIR as three channels (source) and the post-contrast T1 (target) (BraTS 2021).
- [BraTS-Africa adult glioma](https://fidopt.io/dataset/BraTSAfrica/): Brain MR of an adult with a presumed diffuse glioma, scanned at 1.5 T in Nigeria: T1, T1Gd, T2 and FLAIR as one four-channel image on the SRI24 atlas, with three tumour sub-regions labelled (BraTS-Africa).
- [BraTS-PEDs paediatric high-grade glioma](https://fidopt.io/dataset/BraTSPEDs/): Pre-treatment head MR of a child with a high-grade glioma: T1, T1Gd, T2 and FLAIR as one four-channel image on the SRI24 atlas at 1 mm, with four tumour sub-regions labelled (BraTS-PEDs, TCIA).
- [BraTS-Reg](https://fidopt.io/dataset/BraTSReg/): Two contrast-enhanced T1 brain MRs of one patient, before surgery and at follow-up, the follow-up scan being the fixed image (BraTS-Reg).
- [BraTS 2023 meningioma](https://fidopt.io/dataset/BraTS_MEN/): Pre-operative brain MR of a patient with a meningioma, T1, T1Gd, T2 and FLAIR as one four-channel image, with the non-enhancing tumour core, the surrounding FLAIR hyperintensity and the enhancing tumour labelled (ASNR-MICCAI BraTS 2023 meningioma training set, Synapse).
- [Brachial plexus in neck ultrasound videos](https://fidopt.io/dataset/BrachialPlexusUS/): One frame of a patient's neck ultrasound video, 2D, with the supraclavicular or interscalene brachial plexus boxed by anaesthesiologists and shrunk to its outline by an active contour (AIIMS New Delhi and IIIT Hyderabad).
- [BHSD brain haemorrhage CT](https://fidopt.io/dataset/BrainHaemorrhageCT/): Non-contrast head CT of one patient with intracranial haemorrhage from the RSNA Intracranial Hemorrhage Detection data, with five kinds of bleed drawn by medical imaging experts and reviewed by a radiologist (BHSD, test split).
- [Brain-Mets-Lung-MRI-Path-Segs, the resected metastasis](https://fidopt.io/dataset/BrainMetsLungMR/): Pre-operative post-contrast T1 MR of a lung-cancer patient with one brain metastasis at Yale, the metastasis later resected outlined by hand and scored within 20 mm of it (Brain-Mets-Lung-MRI-Path-Segs, TCIA).
- [Pretreat-MetsToBrain-Masks](https://fidopt.io/dataset/BrainMetsMR/): Pretreatment brain MR of a patient with brain metastases at Yale New Haven Hospital: T1, post-contrast T1, T2 and FLAIR as one four-channel image on the SRI24 atlas, every metastasis segmented in three parts.
- [BrainWeb, 20 normal anatomical models](https://fidopt.io/dataset/BrainWeb20/): Two simulated T1-weighted head MR images of two of BrainWeb's 20 digital brain phantoms, each with the tissue classes it was simulated from.
- [BrainWeb, 20 simulated brains, tissue classes](https://fidopt.io/dataset/BrainWebSim/): A simulated T1-weighted head MR of one of BrainWeb's 20 digital brain phantoms, with the eleven tissue classes it was simulated from.
- [BCBM-RadioGenomics, breast cancer brain metastases](https://fidopt.io/dataset/BreastBrainMetsMR/): Post-contrast T1 MR of the brain, skull-stripped, of a patient treated with Gamma Knife radiosurgery for brain metastases of breast cancer at the University of Minnesota, every metastasis outlined for the treatment (BCBM-RadioGenomics, TCIA).
- [Advanced-MRI-Breast-Lesions](https://fidopt.io/dataset/BreastLesionsMR/): Fat-suppressed T1-weighted MR of both breasts at 1.5 T, the second phase after contrast, every suspicious enhancing lesion of the report outlined by a radiologist, thresholded and called tumour or benign (Advanced-MRI-Breast-Lesions, TCIA).
- [Breast-MRI-NACT-Pilot](https://fidopt.io/dataset/BreastNACT/): Fat-suppressed pre-contrast T1 MR of a breast with a tumour, before neoadjuvant chemotherapy (fixed) and after its first cycle (moving) (Breast-MRI-NACT-Pilot, UCSF).
- [CAMUS](https://fidopt.io/dataset/CAMUS/): 2D echocardiography of one patient: an apical two- or four-chamber view at end diastole (fixed) and end systole (moving), with the left ventricular cavity, myocardium and left atrium drawn by a cardiologist on both (CAMUS).
- [CAMUS, 2D echocardiography](https://fidopt.io/dataset/CAMUS_Seg/): 2D echocardiography of one patient, an apical two- or four-chamber view at end diastole or end systole, with the left ventricular cavity, the myocardium and the left atrium drawn by a cardiologist (CAMUS).
- [CARE Planaria, low-exposure to high-exposure fluorescence, 3D](https://fidopt.io/dataset/CAREPlanaria_Syn/): A spinning-disk confocal stack of planarian flatworms stained for their nuclei, taken at 58 times less light (source) and at full light (target), the two conditions interleaved plane by plane in one acquisition (CARE, Weigert et al. 2018).
- [CHAOS CT liver](https://fidopt.io/dataset/CHAOS_CT_Seg/): Portal venous CT of the upper abdomen of a potential liver donor, the liver drawn by hand on every slice (CHAOS, Dokuz Eylul University Hospital).
- [CHAOS MR T1/T2](https://fidopt.io/dataset/CHAOS_MR/): T1-DUAL in-phase (fixed) and T2-SPIR (moving) MR of the upper abdomen of one patient, two series of one study, with the liver, kidneys and spleen drawn on each (CHAOS).
- [CHAOS MR, liver, kidneys and spleen](https://fidopt.io/dataset/CHAOS_MR_Seg/): T1-DUAL in-phase or T2-SPIR MR of one patient's upper abdomen, with the liver, kidneys and spleen drawn by hand (CHAOS).
- [CLEM-Reg, Airyscan fluorescence to volume electron microscopy](https://fidopt.io/dataset/CLEMReg/): One cell specimen imaged twice, an Airyscan fluorescence volume (moving) and a volume electron microscopy (fixed), with manually placed BigWarp correspondences.
- [COBRA2026, CBCT to CT, pelvis](https://fidopt.io/dataset/COBRA2026_CBCTCT_Syn/): Cone-beam CT of one radiotherapy patient's pelvis, reconstructed by the provider from the measured projections, and the planning CT to synthesise from it, registered deformably onto the CBCT by the provider (COBRA2026 training set).
- [COVID-19 CT Lung and Infection](https://fidopt.io/dataset/COVIDLungCT/): One chest CT of a patient with COVID-19 pneumonia, with the left lung, the right lung and the infection drawn by hand and checked by a senior radiologist (COVID-19-CT-Seg, Ma et al. 2021).
- [COph100](https://fidopt.io/dataset/COph100/): Colour retinal photographs of one eye of an infant screened for retinopathy of prematurity, at the last (fixed) and first (moving) of two to nine sessions 2 to 51 weeks apart (COph100, photographs from RIDIRP).
- [CPTAC-CCRCC-Tumor-Annotations](https://fidopt.io/dataset/CPTACCCRCC_Seg/): An abdominal CT of a patient with clear cell renal cell carcinoma before treatment, the kidney tumours outlined by radiologists and reviewed by board-certified radiologists (CPTAC-CCRCC-Tumor-Annotations on CPTAC-CCRCC, TCIA).
- [CPTAC-PDA-Tumor-Annotations](https://fidopt.io/dataset/CPTACPDALesions/): Abdominal CT of a patient with a pancreatic ductal adenocarcinoma before treatment, the primary tumour outlined by radiologists and reviewed by board-certified radiologists (CPTAC-PDA-Tumor-Annotations on CPTAC-PDA, TCIA).
- [CPTAC-UCEC-Tumor-Annotations](https://fidopt.io/dataset/CPTACUCECLesions/): A post-contrast T1-weighted pelvic MR of a woman with endometrial carcinoma before treatment, the uterus holding the tumour outlined as a target lesion by radiologists and reviewed by board-certified radiologists (CPTAC-UCEC-Tumor-Annotations on CPTAC-UCEC, TCIA).
- [CRASAR-U-DROIDs, drone and crewed aerial registration](https://fidopt.io/dataset/CRASAR_UDROIDs/): A native drone RGB orthomosaic of an area hit by a hurricane and the crewed aircraft image of the same area, with building correspondences derived from human local alignment corrections (CRASAR-U-DROIDs).
- [CREMI sections, known in-plane deformation](https://fidopt.io/dataset/CREMI/): A section of a serial-section TEM volume of an adult Drosophila brain (CREMI test volumes A+, B+, C+) paired with a known smooth deformation of itself: it measures the recovery of a known in-plane warp, not the alignment of adjacent sections.
- [CREMI synaptic clefts](https://fidopt.io/dataset/CREMIClefts/): A block of a serial-section TEM volume of an adult Drosophila brain, 4 x 4 x 40 nm a voxel, its synaptic clefts segmented by hand and merged into one label (CREMI).
- [Colorectal-Liver-Metastases, liver and veins](https://fidopt.io/dataset/CRLMCT/): Preoperative portal-venous CT of the liver of two patients with colorectal liver metastases, paired by us, with the liver and its hepatic and portal veins segmented (Colorectal-Liver-Metastases, Memorial Sloan Kettering).
- [Colorectal-Liver-Metastases, liver and veins](https://fidopt.io/dataset/CRLMCT_Seg/): Portal venous CT of one patient with colorectal liver metastases, with the liver, the hepatic veins and the portal veins segmented (Colorectal-Liver-Metastases).
- [CSI 2014 vertebrae](https://fidopt.io/dataset/CSI2014Vertebrae/): Spine CT of a young adult or of a patient with vertebral compression fractures, each thoracic and lumbar vertebra segmented (CSI 2014 vertebra segmentation challenge, University of California, Irvine).
- [CSXA cervical radiographs](https://fidopt.io/dataset/CSXA/): Lateral radiographs of the cervical spine of two people, with 23 keypoints on the vertebral bodies of C2 to C7 placed and checked by spine surgeons on each (Cervical Spine X-ray Atlas, Dongzhimen Hospital, Beijing).
- [CT Colonography (ACRIN 6664)](https://fidopt.io/dataset/CTColonography/): CT colonography of one patient, prone (fixed) and supine (moving) in one exam, the colon distended with gas (ACRIN 6664, the National CT Colonography Trial).
- [CT Lymph Nodes, abdomen](https://fidopt.io/dataset/CTLymphNodes_Abdomen/): Contrast-enhanced CT of the chest, abdomen and pelvis of an NIH Clinical Center patient, with the marked lymph nodes of the abdomen and pelvis, most of them enlarged, traced by hand (CT Lymph Nodes).
- [CT Lymph Nodes, mediastinum](https://fidopt.io/dataset/CTLymphNodes_Mediastinum/): A contrast-enhanced CT of the chest, abdomen and pelvis of an NIH Clinical Center patient, the marked enlarged lymph nodes of the mediastinum traced by hand (CT Lymph Nodes, the 90 MED_LYMPH patients).
- [CT-ORG](https://fidopt.io/dataset/CTORG/): Abdomen-pelvis, chest-abdomen-pelvis or whole-body CT of a patient with lesions in the liver or another labelled organ, with the liver, bladder, lungs, kidneys, bones and brain segmented (CT-ORG).
- [CT-ORG, pairs of patients](https://fidopt.io/dataset/CTORG_Reg/): CT scans of two patients from CT-ORG, each on its own grid, with up to six organs labelled: liver, urinary bladder, lungs, kidneys, bone and brain.
- [CTPelvic1K, CLINIC pelvic bones](https://fidopt.io/dataset/CTPelvic1K_Clinic/): One preoperative pelvic CT from the CLINIC sub-dataset of CTPelvic1K, with the sacrum and the two hip bones annotated through an iterative network-and-expert correction workflow.
- [C-TRUS, colon wall in transabdominal ultrasound](https://fidopt.io/dataset/CTRUS/): A transabdominal B-mode image of the colon of a patient with ulcerative colitis, 2D, with the colon wall outlined by a gastroenterologist (C-TRUS, University of Münster).
- [CTSpine1K](https://fidopt.io/dataset/CTSpine1K/): CT of one patient from one of four public collections (CT colonography, liver tumour CT, COVID-19 chest CT, head and neck CT), with each vertebra in the field segmented, C1 to L6 (CTSpine1K).
- [Calgary-Campinas-359, T1 brain MR between subjects](https://fidopt.io/dataset/CalgaryCampinas/): T1-weighted head MR of two healthy adults scanned on the same scanner model (Siemens, Philips or GE, 1.5 or 3 T), with FastSurfer's anatomical labels on both (CC-359).
- [Calgary-Campinas-359, manual brain masks](https://fidopt.io/dataset/CalgaryCampinas_Seg/): One T1-weighted head MR of a healthy adult, from a Siemens, Philips or GE scanner at 1.5 or 3 T, with the brain mask an expert drew by hand (CC-359).
- [CancerVerse](https://fidopt.io/dataset/CancerVerseCT/): A CT of the abdomen, pelvis or chest of a patient with a cancer of one of 13 organs, from hospitals in Switzerland and Turkey, with every tumour of those organs drawn by radiology residents and reviewed by board-certified radiologists (CancerVerse 3.5.1).
- [CC-Tumor-Heterogeneity](https://fidopt.io/dataset/CervixMR/): Sagittal T2 MR of the pelvis of one patient with advanced cervical cancer, before chemoradiotherapy (fixed) and 2 to 2.5 weeks into it (moving), from CC-Tumor-Heterogeneity (TCIA).
- [CC-Tumor-Heterogeneity, cervical tumour](https://fidopt.io/dataset/CervixMR_Seg/): Sagittal T2 MR of the pelvis of one patient with advanced cervical cancer before chemoradiotherapy, with the tumour drawn by hand (CC-Tumor-Heterogeneity, TCIA).
- [Aphasia Recovery Cohort stroke lesions](https://fidopt.io/dataset/ChronicStrokeT2/): T2-weighted brain MR of a person with aphasia, months to years after a left-hemisphere stroke, with the chronic lesion drawn by an expert (Aphasia Recovery Cohort, University of South Carolina, OpenNeuro ds004884).
- [CirrMRI600+, cirrhotic liver on T2-weighted MR](https://fidopt.io/dataset/CirrhoticLiverMR/): A T2-weighted abdominal MR of a patient with liver cirrhosis, from one centre in Istanbul, with the liver outlined (CirrMRI600+).
- [Claustrum at 7 T](https://fidopt.io/dataset/Claustrum7T/): A brain-masked 7 T MP2RAGE image of a healthy adult volunteer at Maastricht University, 0.7 or 1.0 mm, with the claustrum on each side drawn by hand (Calarco et al. 2026).
- [Colorectal cancer TMA cores, H&E to CD44](https://fidopt.io/dataset/ColorectalTMAStains/): One tissue-microarray core of a colorectal cancer, two sections of it scanned whole at 40x: haematoxylin and eosin (fixed) and CD44 immunohistochemistry (moving), with the provider's automatic epithelium mask on each.
- [DeePiCt S. pombe cryo-electron tomograms](https://fidopt.io/dataset/CryoETPombe/): A cryo-electron tomogram of a FIB-milled lamella of a fission yeast cell (S. pombe), at 2.7 nm a voxel, with its organelles and cytoplasm segmented or corrected by hand (DeePiCt, CryoET Data Portal).
- [DDTI, thyroid nodules outlined on ultrasound](https://fidopt.io/dataset/DDTI/): A 2D B-mode thyroid ultrasound image of a patient's nodule, described with TI-RADS by radiologists of IDIME (Bogotá) and outlined in the provider's web tool: one image a case of DDTI's first version (Pedraza et al. 2015).
- [2D DIC Challenge 1.0](https://fidopt.io/dataset/DICChallenge2D/): A speckle pattern's reference image (fixed) and an image of it moved by a known sub-pixel to few-pixel displacement (moving), from the 2D Digital Image Correlation Challenge 1.0.
- [spatialLIBD DLPFC Visium, adjacent sections](https://fidopt.io/dataset/DLPFCVisium/): Two adjacent H&E sections, 10 µm apart, of one adult's dorsolateral prefrontal cortex on 10x Visium slides, with the cortical layer people assigned to each spot (spatialLIBD, Maynard et al. 2021).
- [Data Science Bowl 2018, nuclei of many experiments](https://fidopt.io/dataset/DSB2018Nuclei/): One 2D light-microscopy image of stained nuclei, fluorescence or histology, from one biological experiment of the 2018 Data Science Bowl, every nucleus drawn by hand (BBBC038v1).
- [DeepCLEM, fluorescence and SEM with a known deformation](https://fidopt.io/dataset/DeepCLEM/): A fluorescence and a scanning electron microscopy image of one C. elegans section, aligned by hand by the provider, the SEM image deformed by a seeded smooth warp whose recovery is measured.
- [DeepLIIF, IHC to DAPI with known deformation](https://fidopt.io/dataset/DeepLIIF/): A 2D lung or bladder tile of one tissue section: Ki67 IHC (fixed) and DAPI (moving) as the authors registered them, the DAPI then deformed by a known warp (DeepLIIF).
- [Digital Hand Atlas radiographs](https://fidopt.io/dataset/DigitalHandAtlas/): Left-hand and wrist radiographs of two children, 2D films digitised by the USC Image Processing and Informatics Lab, with 37 landmarks on the fingertips, finger joints and wrist placed by Payer et al. on each (Digital Hand Atlas).
- [DoseRAD2026, MR to CT, thorax and abdomen](https://fidopt.io/dataset/DoseRAD2026_MRCT_Syn/): 0.35 T MR-Linac MR (bSSFP) of one patient and the CT to synthesise from it, the CT registered deformably to the MR by the provider (DoseRAD2026 training set, SynthRAD2025 centre B).
- [Duke intermediate AMD SD-OCT, retina and RPEDC](https://fidopt.io/dataset/DukeAMDOCT/): The B-scan through the fovea of a macular SD-OCT volume of an eye with intermediate age-related macular degeneration or of a control, with the retina and the retinal pigment epithelium and drusen complex marked (Farsiu et al. 2014, Duke).
- [Duke breast MRI, breast tissues](https://fidopt.io/dataset/DukeBreastFGT/): The fat-saturated T1-weighted MR before contrast of a woman with invasive breast cancer at Duke, with the breasts' fatty tissue, fibroglandular tissue and vessels drawn by hand (Duke-Breast-Cancer-MRI's 3D segmentations, Lew et al. 2024).
- [Duke breast DCE MR, pre-contrast to first post-contrast](https://fidopt.io/dataset/DukeBreastMR_Syn/): Fat-saturated T1-weighted breast MR of a woman with invasive breast cancer before surgery: the pre-contrast series (source) and the first post-contrast series (target) of one dynamic examination, on one grid (Duke-Breast-Cancer-MRI, TCIA).
- [ENHANCE.PET 1.6k, CT to PET](https://fidopt.io/dataset/ENHANCEPET_CTPET_Syn/): The CT (source) and the FDG-PET in SUV (target) of one whole-body PET/CT session of a patient with lung cancer at University Hospital Leipzig, on the PET's grid (ENHANCE.PET 1.6k).
- [ETH3D high-res multi-view](https://fidopt.io/dataset/ETH3D/): Two DSLR photographs of one indoor or outdoor scene from nearby viewpoints: the middle photograph of an ETH3D high-res multi-view training scene (fixed) and the one sharing the most keypoints with it (moving).
- [ENHANCE.PET 1.6k](https://fidopt.io/dataset/EnhancePETBodyCT/): The CT of a whole-body FDG-PET/CT study of a patient with lung cancer at Leipzig or Careggi, with 127 structures (organs, heart and vessels, muscles, bones, ribs, vertebrae) drafted by a network and corrected by people (ENHANCE.PET 1.6k).
- [Ex vivo medial temporal lobe MRI (Penn)](https://fidopt.io/dataset/ExVivoMTL/): Fixed temporal lobe specimens of two donors from one brain bank, T2-weighted MR at 9.4 T and 0.2 mm, with the medial temporal lobe cortex segmented on each (OpenNeuro ds004767, Ravikumar et al. 2024).
- [Bonn focal cortical dysplasia (FLAIR)](https://fidopt.io/dataset/FCDBonnFLAIR/): FLAIR MR of the brain of a person with epilepsy due to a focal cortical dysplasia type II, the dysplastic cortex outlined by a neurologist and reviewed by another (University Hospital Bonn, OpenNeuro ds004199).
- [FIMD](https://fidopt.io/dataset/FIMD/): Colour fundus photographs of one child's eye as myopia developed (FIMD): the first visit at 6 or 7 years old (fixed) and the last, four or five years later, on another camera (moving).
- [FIRE](https://fidopt.io/dataset/FIRE/): Two colour photographs of one eye's retina, from two viewpoints in one examination or at two examinations with changes between: the reference (fixed) and test (moving) image of a Fundus Image Registration pair.
- [FIVES, retinal vessels drawn by hand](https://fidopt.io/dataset/FIVES/): A colour photograph of the retina, 2D, with its vessels painted by two trained annotators and corrected by an ophthalmic practitioner: one of the 800 images of FIVES (Second Affiliated Hospital of Zhejiang University), 200 each normal, AMD, diabetic retinopathy and glaucoma.
- [FLARE22](https://fidopt.io/dataset/FLARE22/): Portal venous abdominal CT of a patient before resection of a pancreatic mass at Memorial Sloan Kettering (the decathlon's Task07 Pancreas), with 13 abdominal organs segmented for the FLARE 2022 challenge.
- [FUGC, the cervical lips on transvaginal ultrasound](https://fidopt.io/dataset/FUGC/): A 2D transvaginal ultrasound image of the uterine cervix with its anterior and posterior lips outlined, drafted by a fine-tuned SAM and refined by an obstetric sonographer: one examination of the FUGC challenge (ISBI 2025, Jinan University), its first image.
- [FUMPE, pulmonary embolism](https://fidopt.io/dataset/FUMPE/): A CT pulmonary angiogram of a patient with pulmonary embolism in Mashhad, Iran, with the emboli outlined by a radiologist (FUMPE).
- [Fedorov prostate MRI and TRUS, three annotated cases](https://fidopt.io/dataset/FedorovMRTRUS/): One prostate MRI and transrectal ultrasound pair released by SPL and NCIGT, with whole-gland contours and named internal anatomical fiducials.
- [UTSW-Glioma, adult glioma before surgery](https://fidopt.io/dataset/GliomaUTSWMR/): Brain MR of an adult with a glioma before any resection: T1, T1Gd, T2 and FLAIR as one four-channel image, registered to SRI24 and skull-stripped, with necrotic core, oedema and enhancing tumour labelled (UTSW-Glioma, TCIA).
- [HC18, the fetal head as a sonographer measured it](https://fidopt.io/dataset/HC18/): A 2D ultrasound image of the fetal head in its standard plane with the ellipse an experienced sonographer drew around the skull to measure the head circumference, filled: one examination of HC18 (Radboud University Medical Center, 2014 to 2015).
- [HCC-TACE-Seg](https://fidopt.io/dataset/HCCTACE/): Contrast-enhanced liver CT of a patient with hepatocellular carcinoma, 1 to 12 weeks before a first transarterial chemoembolisation at MD Anderson Cancer Center, with the liver, tumour and intrahepatic vessels segmented (HCC-TACE-Seg).
- [Head Neck CBCT CT (HUST)](https://fidopt.io/dataset/HNCBCTCT/): Planning CT (fixed) and first-day cone-beam CT (moving) of one head and neck radiotherapy patient at Huazhong University of Science and Technology.
- [Head Neck CBCT to CT (HUST)](https://fidopt.io/dataset/HNCBCTCT_Syn/): First-day cone-beam CT (source) and planning CT (target) of one head and neck radiotherapy patient, the CBCT registered onto the CT by the corpus (Huazhong University of Science and Technology).
- [Weekly ADC on the MR-Linac, head and neck](https://fidopt.io/dataset/HNMRLinacADC/): ADC maps of the neck of one head and neck cancer patient on a 1.5 T MR-Linac, before radiotherapy (fixed) and in its third week (moving), from MD Anderson's weekly intra-treatment DWI dataset.
- [HNTS-MRG 2024](https://fidopt.io/dataset/HNTSMRG/): Two T2-weighted neck MRs of one patient with head and neck cancer, before radiotherapy (fixed) and two to four weeks into it (moving) (HNTS-MRG 2024 training set).
- [HNTS-MRG 2024, pretreatment tumour segmentation](https://fidopt.io/dataset/HNTSMRG_Seg/): Pretreatment T2 MRI of the head and neck of one patient, with consensus contours of the primary tumour and the involved lymph nodes: the native fixed images of HNTSMRG.
- [HPatches](https://fidopt.io/dataset/HPatches/): Two colour photographs of one planar scene, a poster, print, mural or wall, from two viewpoints: a viewpoint sequence's reference image (fixed) and its last target image (moving), from HPatches.
- [HQColon](https://fidopt.io/dataset/HQColon/): CT colonography of one patient, supine (fixed) and prone (moving) in one exam, the colon distended with gas and segmented whole on both scans (HQColon masks on TCIA's CT COLONOGRAPHY, ACRIN 6664).
- [HQColon, colon](https://fidopt.io/dataset/HQColon_Seg/): CT colonography of one patient, with the whole colon segmented, its gas- and fluid-filled parts together (HQColon).
- [HVSMR-2.0](https://fidopt.io/dataset/HVSMR/): Whole-heart 3D cardiovascular MR at 1.5 T of one child or adult with congenital heart disease, cropped around the heart, with its four chambers and four great vessels labelled (HVSMR-2.0).
- [HaN-Seg](https://fidopt.io/dataset/HaNSeg/): Planning CT of the head and neck of one radiotherapy patient at the Institute of Oncology Ljubljana, with 30 organs at risk delineated by experts and curated (HaN-Seg, public set 1).
- [HaN-Seg, T1 MR to CT](https://fidopt.io/dataset/HaNSeg_Syn/): T1-weighted MR (source) and planning CT (target) of the head and neck of one radiotherapy patient at the Institute of Oncology Ljubljana, the MR registered onto the CT by the corpus (HaN-Seg, public set 1).
- [PIANO hand MRI](https://fidopt.io/dataset/HandMR/): T1-weighted MR of one person's right hand in two poses, each held in a mould, paired by us (PIANO hand MRI dataset, part 1).
- [PIANO hand MRI, bones](https://fidopt.io/dataset/HandMR_Seg/): MR of one hand in one pose with its bones as one mask (PIANO).
- [TotalSegmentator hip_implant, CT](https://fidopt.io/dataset/HipImplantCT/): A CT of one hip carrying an implant, at the resolution it was reconstructed at, the implant segmented, from the training set of TotalSegmentator's task hip_implant.
- [Hippocampal subfields on 7T T2w MR (Beijing)](https://fidopt.io/dataset/HippoSubfields7T/): 7 T T2-weighted MR around both hippocampi of a healthy young adult, with seven subfields drawn by hand on every coronal slice of each side (Chu et al., Scientific Data 2025, figshare+ 26075713).
- [ICASSP-2024 3D-CBCT challenge, simulated low-dose CBCT to CT](https://fidopt.io/dataset/ICASSPCBCT_Syn/): Chest cone-beam CT simulated at a tenth of the clinical dose from a LIDC-IDRI CT (source) and the noiseless reconstruction of the same simulated scan (target), on one grid (ICASSP-2024 3D-CBCT challenge, validation set).
- [Image Matching Challenge PhotoTourism](https://fidopt.io/dataset/IMCPhotoTourism/): Two tourists' photographs of one landmark, taken years apart with different cameras: the two images of one of the Image Matching Challenge 2021's PhotoTourism stereo pairs.
- [3D-IRCADb-01](https://fidopt.io/dataset/IRCADb01/): Abdominal CT of an adult, three in four with liver tumours, the liver and its tumours segmented (3D-IRCADb-01, IRCAD Strasbourg).
- [ISBI 2012 EM sections, known in-plane deformation](https://fidopt.io/dataset/ISBI2012EM/): A section of a serial-section TEM stack of a Drosophila first instar larva's ventral nerve cord paired with a known smooth deformation of itself: it measures the recovery of a known in-plane warp, not the alignment of adjacent sections.
- [ISIC 2018, skin lesions outlined on dermoscopy](https://fidopt.io/dataset/ISIC2018/): A dermoscopic colour photograph of a pigmented skin lesion with the outline of its one primary lesion, made by hand or by an algorithm and reviewed by dermatologists (ISIC 2018 challenge, Task 1).
- [ISLES 2022](https://fidopt.io/dataset/ISLES2022/): Skull-stripped diffusion-weighted brain MR (b=1000) of a patient with an acute or sub-acute ischaemic stroke, the lesions traced and approved by neuroradiologists (ISLES 2022 training set, Munich and Bern).
- [ISLES 2022, diffusion to FLAIR](https://fidopt.io/dataset/ISLES2022_Syn/): The diffusion-weighted brain MR (b=1000) and ADC map of a patient with an acute or sub-acute ischaemic stroke, and the FLAIR of the same session, registered onto them by the corpus, as the target (ISLES 2022 training set, Munich and Bern).
- [ISLES'24 final infarct, DWI and ADC](https://fidopt.io/dataset/ISLES2024/): Follow-up brain diffusion MR of a patient 2 to 9 days after thrombectomy for an acute ischaemic stroke: the DWI trace image and the ADC map, registered by the provider onto the admission CT, as one two-channel image, with the final infarct masked (ISLES'24 training set, Munich and Zurich).
- [ISLES'24, non-contrast CT to CT angiography](https://fidopt.io/dataset/ISLES24_NCCTCTA_Syn/): Admission non-contrast head CT (source) and CT angiography (target) of a patient with an acute ischaemic stroke, the angiography registered rigidly onto the non-contrast CT and resampled onto its grid by the provider (ISLES'24 training set, Munich and Zurich).
- [ISLES 2016 and 2017, final infarct from acute MR](https://fidopt.io/dataset/ISLESOutcomeMR/): Acute diffusion and perfusion maps of a patient with an ischaemic stroke of the middle cerebral artery, with the final infarct a neuroradiologist drew on the 90-day follow-up (ISLES 2017 training set, Bern and Freiburg).
- [ISPY1-Tumor-SEG-Radiomics](https://fidopt.io/dataset/ISPY1BreastMR/): First post-contrast phase of the pre-treatment breast DCE MR of a woman with locally advanced breast cancer, the whole primary tumour outlined by hand and approved by a breast radiologist (ISPY1-Tumor-SEG-Radiomics, TCIA).
- [I-SPY 2 DCE MR, pre-contrast to early post-contrast](https://fidopt.io/dataset/ISPY2_Syn/): Fat-suppressed T1-weighted breast MR of a woman with locally advanced breast cancer before treatment: the pre-contrast phase (source) and the early post-contrast phase (target) of one dynamic acquisition, on one grid (ISPY2, TCIA).
- [IXI T2 to PD](https://fidopt.io/dataset/IXI_T2PD/): T2-weighted (source) and proton-density-weighted (target) MR of the head of one healthy subject, the two echoes of one acquisition (IXI).
- [IXI, TransMorph atlas-to-subject release](https://fidopt.io/dataset/IXI_TransMorph/): A skull-stripped, affinely aligned T1-weighted IXI brain (moving) and the shared CycleMorph atlas (fixed), from TransMorph's release, with automatic FreeSurfer aseg labels on both.
- [In silico labeling, transmitted light to nucleus fluorescence, 2D](https://fidopt.io/dataset/InSilicoLabeling_Syn/): One well of a cell culture in 2D: the middle plane of a transmitted-light z-stack (bright field, phase contrast or DIC) as source, and the maximum projection of the nucleus stain's fluorescence of the same field as target (In silico labeling, Google and the Finkbeiner and Rubin labs).
- [Human Inner Ear Anatomy](https://fidopt.io/dataset/InnerEarCT/): Two cadaver temporal bones scanned by volume CT at 0.0986 mm, with the inner ear's fluid space labelled by hand (Human Inner Ear Anatomy).
- [Human inner ear CT, fluid spaces](https://fidopt.io/dataset/InnerEarCT_Seg/): Flat-panel volume CT at 0.0986 mm of one cadaver temporal bone, with the inner ear's fluid space labelled by hand: cochlea, vestibule, semicircular canals.
- [Serial sections, mouse prostate and liver (Kartasalo 2018)](https://fidopt.io/dataset/KartasaloHistology/): Two consecutive sections of one paraffin block, a mouse prostate or liver, stained with haematoxylin and eosin and scanned at 0.46 µm a pixel, with four point pairs placed by people (Kartasalo et al. 2018).
- [KiTS23](https://fidopt.io/dataset/KiTS23/): A preoperative contrast-enhanced abdominal CT of a patient operated on or ablated for a suspected kidney cancer in the M Health Fairview system, Minnesota, with the kidneys, tumours and cysts segmented (KiTS23 training set).
- [KiTS23 CT/CT](https://fidopt.io/dataset/KiTS23_CTCT/): Preoperative contrast-enhanced abdominal CTs of two patients operated on or ablated for a suspected kidney cancer in the M Health Fairview system, Minnesota, paired by us from KiTS23's training set, with TotalSegmentator's organs on both and the provider's kidneys.
- [C4KC-KiTS](https://fidopt.io/dataset/KiTSCT/): Late arterial abdominal CT of a patient before the removal of a kidney tumour at the University of Minnesota, with the kidneys and the tumour segmented (C4KC-KiTS on TCIA, KiTS19's training set).
- [T2-weighted Kidney MRI](https://fidopt.io/dataset/KidneyT2MR/): Coronal T2-weighted MR of the kidneys of a healthy volunteer or a patient with chronic kidney disease, both kidneys traced by hand as one label (University of Nottingham, Daniel et al. 2021).
- [OAIZIB-CM](https://fidopt.io/dataset/KneeMR/): Sagittal 3D DESS MR of the right knee of two adults of the Osteoarthritis Initiative at baseline, paired by us, with the femur, the tibia and their cartilage labelled (OAIZIB-CM).
- [OAIZIB-CM, knee bones and cartilage](https://fidopt.io/dataset/KneeMR_Seg/): Sagittal 3D DESS MR of the right knee of one adult of the Osteoarthritis Initiative, with the femur, the tibia and their cartilage labelled (OAIZIB-CM).
- [Kvasir-SEG, colonoscopy polyps outlined by hand](https://fidopt.io/dataset/KvasirSEG/): A white-light colonoscopy photograph, 2D and in colour, with its polyps outlined: pre-segmented by a junior doctor and a PhD student, then corrected by a gastroenterologist (Kvasir-SEG, Bærum Hospital, Norway).
- [Learn2Reg 2020, Task 3, validation](https://fidopt.io/dataset/L2R_AbdomenCTCT/): Abdominal CT scans of two different patients, a validation pair of Learn2Reg 2020 Task 3, with 13 labels on both.
- [Abdomen CT (Learn2Reg 2020, Task 3)](https://fidopt.io/dataset/L2R_AbdomenCTCT_Seg/): Abdominal CT of one patient with 13 organs labelled (the Learn2Reg 2020 abdomen task, from the Multi-Atlas Labeling Beyond the Cranial Vault challenge).
- [Learn2Reg 2021, AbdomenMRCT, validation](https://fidopt.io/dataset/L2R_AbdomenMRCT/): An abdominal MR, fixed, and CT, moving, of one patient, with four organs labelled and ROI masks, from Learn2Reg 2021 Task 1's validation.
- [Abdomen CT (Learn2Reg 2021, AbdomenMRCT)](https://fidopt.io/dataset/L2R_AbdomenMRCT_SegCT/): Abdominal CT of one patient with the liver, the spleen and the kidneys labelled (the Learn2Reg 2021 abdomen MR/CT task).
- [Abdomen MR (Learn2Reg 2021, AbdomenMRCT)](https://fidopt.io/dataset/L2R_AbdomenMRCT_SegMR/): Abdominal MR of one patient with the liver, the spleen and the kidneys labelled (the Learn2Reg 2021 abdomen MR/CT task).
- [Learn2Reg 2021 AbdomenMRCT, MR to CT](https://fidopt.io/dataset/L2R_AbdomenMRCT_Syn/): Abdominal MR (source) and CT (target) of one patient, the challenge's paired images on its 2 mm grid, the MR registered onto the CT by the corpus (Learn2Reg 2021, AbdomenMRCT).
- [Learn2Reg 2020, Task 4, validation](https://fidopt.io/dataset/L2R_HippocampusMR/): Hippocampus MR crops of two people, with the head and the tail of the hippocampus labelled (Learn2Reg 2020 Task 4, from the Medical Segmentation Decathlon).
- [Hippocampus MR (Learn2Reg 2020, Task 4)](https://fidopt.io/dataset/L2R_HippocampusMR_Seg/): MR crop around one hippocampus of one adult, with its head and its tail labelled (the Medical Segmentation Decathlon's hippocampus images, as Learn2Reg 2020 prepared them).
- [Learn2Reg 2021, LungCT, validation](https://fidopt.io/dataset/L2R_LungCT/): Lung CT of one patient at exhale (fixed) and inhale (moving), with manual landmarks (Learn2Reg 2021 Task 2, LungCT, validation).
- [NLST (Learn2Reg 2022-23), validation](https://fidopt.io/dataset/L2R_NLST/): Baseline CT (fixed) and follow-up CT (moving) of the lungs of one NLST participant, a validation pair of Learn2Reg 2022/23, with the challenge's public corrField keypoints.
- [Learn2Reg 2021, OASIS, validation](https://fidopt.io/dataset/L2R_OASIS/): Brain MR of two subjects of OASIS, a validation pair of Learn2Reg 2021 Task 3, with 35 labelled structures.
- [ThoraxCBCT (Learn2Reg 2023), validation](https://fidopt.io/dataset/L2R_ThoraxCBCT/): One Learn2Reg 2023 ThoraxCBCT validation pair on the board's 1 mm grid, CBCT fixed and FBCT moving, with the Dec 2023 validation labels (13 of the 15 classes) and manual landmarks (fixed_keypoints.csv: Dec 2023 keypoints).
- [LASC 2013 MRI](https://fidopt.io/dataset/LASC2013/): Whole-heart 3D bSSFP MRI at 1.5 T, with the left atrium, a short part of its appendage and the proximal sections of its four pulmonary veins segmented as one label (Left Atrial Segmentation Challenge 2013).
- [2018 Left Atrium Segmentation Challenge](https://fidopt.io/dataset/LASeg2018/): 3D late gadolinium-enhanced MRI of the left atrium of a patient with atrial fibrillation, before or after ablation, the atrial cavity traced by hand (2018 Atrial Segmentation Challenge, University of Utah).
- [LCTSC](https://fidopt.io/dataset/LCTSC/): Radiotherapy planning CTs of the thorax of two patients of one institution, with five organs at risk contoured on both (Lung CT Segmentation Challenge, AAPM 2017), paired by us.
- [LCTSC, thoracic organs at risk](https://fidopt.io/dataset/LCTSC_Seg/): Radiotherapy planning CT of one patient's thorax, with five organs at risk contoured by hand (AAPM Lung CT Segmentation Challenge 2017).
- [LIDC-IDRI](https://fidopt.io/dataset/LIDCNodules/): Chest CT of one LIDC-IDRI patient with the lung nodules of 3 mm or more that at least two of its four thoracic radiologists outlined, read from the DICOM SEGs of DICOM-LIDC-IDRI-Nodules (TCIA).
- [LNDb](https://fidopt.io/dataset/LNDbNodules/): Chest CT of an adult from the São João University Hospital Centre in Porto, with the lung nodules of 3 mm or more segmented by one radiologist (LNDb, the training set of the LNDb challenge).
- [LUMINOUS, lumbar multifidus in ultrasound](https://fidopt.io/dataset/LUMINOUS/): A transverse B-mode image of a young athlete's lower back at L5, 2D, with the lumbar multifidus outlined by hand on one or both sides (LUMINOUS, Concordia University).
- [LUMIR (Learn2Reg 2024), training images](https://fidopt.io/dataset/LUMIR/): Brain T1 MR of two healthy subjects from OpenBHB, skull-stripped and linearly registered to MNI152 by the LUMIR organisers.
- [LUNA25](https://fidopt.io/dataset/LUNA25/): Low-dose chest CT of one participant at two rounds of the National Lung Screening Trial, with the nodules annotated on both scans (LUNA25 public training and development set).
- [LV infarct scar on LGE MR (MICCAI 2012 challenge)](https://fidopt.io/dataset/LVScarLGE/): A short-axis late gadolinium-enhanced MR stack of the left ventricle of a patient or a pig after a myocardial infarction, the myocardium given as a mask and the scar outlined by a consensus of three cardiologists (Karim et al. 2016).
- [Lower leg muscles, 3D ultrasound](https://fidopt.io/dataset/LegMuscleUS/): Freehand 3D ultrasound of a healthy volunteer's calf, compounded from four to six tracked sweeps with the leg in a water bath, the soleus and both gastrocnemius heads labelled (Leg-3D-US, Nantes University and TU Munich).
- [Light My Cells, transmitted light to nucleus fluorescence, 2D](https://fidopt.io/dataset/LightMyCells_Nucleus_Syn/): One field of a cell culture in 2D: a transmitted-light image (bright field, phase contrast or DIC) as source, and the nucleus fluorescence image of the same field and focal plane as target (Light My Cells, France-BioImaging).
- [Liver-DIR-QA](https://fidopt.io/dataset/LiverDIRQA/): Contrast-enhanced CT of the abdomen and pelvis of one patient at two dates, 12 to 1499 days apart, with vessel bifurcations paired inside the liver (Liver-DIR-QA).
- [LiverHccSeg, arterial liver MR](https://fidopt.io/dataset/LiverHCCMR/): Arterial-phase liver MR of one patient with hepatocellular carcinoma from TCGA-LIHC, the liver and the tumour delineated by hand. The arterial image is used as delivered, without the provider's warps of the other phases.
- [TotalSegmentator liver_lesions, CT](https://fidopt.io/dataset/LiverLesionsCT/): Contrast-enhanced abdominal CT of a University Hospital Basel patient whose radiology report mentions a liver lesion, every liver lesion segmented under one label (TotalSegmentator's liver_lesions training set).
- [Liver lesions, curated MRI subset](https://fidopt.io/dataset/LiverLesionsMR/): One liver MR scan, most often a contrast-enhanced T1, with a manual liver-lesion mask, from the MR part of the mixed-modality archive released for TotalSegmentator liver_lesions_mr.
- [CT follow-up of liver metastases](https://fidopt.io/dataset/LiverMetsCT/): Portal-venous abdominal CTs of one patient with liver metastases, before and after systemic chemotherapy, 32 to 287 days apart (Al-Zahra Hospital, Isfahan).
- [CT follow-up of liver metastases, liver](https://fidopt.io/dataset/LiverMetsCT_Seg/): Abdominal CT of one patient followed for liver metastases, with the liver and its metastases as one mask.
- [PLC-CECT](https://fidopt.io/dataset/LiverPhasesCT/): Contrast-enhanced liver CT of one patient with primary liver cancer before treatment: the delayed phase (fixed) and the arterial phase (moving) of one examination (PLC-CECT, Chongqing Yubei District People's Hospital).
- [PLC-CECT, delayed-phase liver segmentation](https://fidopt.io/dataset/LiverPhasesCT_Seg/): The delayed contrast phase of a primary liver cancer CT examination, with the liver label refined by clinicians: the fixed images of LiverPhasesCT, referenced on their native grid without copying or resampling.
- [TotalSegmentator liver segments MR](https://fidopt.io/dataset/LiverSegmentsMR/): An abdominal MR of one patient, from the University Hospital Basel or the Imaging Data Commons, of many sequences and orientations, the eight Couinaud liver segments drawn by hand (TotalSegmentator's liver_segments_mr training set, version 2.0.0).
- [Liver 3D US-CT](https://fidopt.io/dataset/LiverUSCT/): 3D ultrasound of the liver (fixed) and contrast-enhanced abdominal CT (moving) of one patient, from two hospitals and two ultrasound devices (the training data of 3D SA-LoIFM).
- [Longitudinal-CT](https://fidopt.io/dataset/LongitudinalCT/): Whole-body contrast CT of one melanoma patient at baseline (fixed) and at follow-up under systemic therapy (moving), with every lesion segmented and linked between the two times (Longitudinal-CT, autoPET IV task 2).
- [VSDFullBodyBoneReconstruction](https://fidopt.io/dataset/LowerBodyBonesCT/): A forensic post-mortem CT from the forensic institutes of Bern and Zurich, from the lower lumbar spine to the toes, with its 21 bones segmented (Fischer 2023, on the Virtual Skeleton Database's CTs).
- [Lucchi++, mitochondria of the mouse hippocampus](https://fidopt.io/dataset/LucchiMitoEM/): A block of a FIB-SEM volume of mouse CA1 hippocampus, 5 nm a voxel, its mitochondria segmented by hand (EPFL, re-annotated as Lucchi++).
- [Multi-scanner lumbar T1 MRI, vertebrae and discs](https://fidopt.io/dataset/LumbarMultiScannerMR/): A native non-contrast T1 lumbar MRI of one patient, with the L1 to L5 vertebral bodies and the four discs between them delineated by hand.
- [Lung250M-4B](https://fidopt.io/dataset/Lung250M/): Chest CT of one patient, inspiration and expiration or baseline and follow-up, with manual landmarks (Lung250M-4B validation pairs).
- [4D-Lung, tumour and lymph nodes on 4D CT](https://fidopt.io/dataset/Lung4DCT_Seg/): One respiratory phase of a 4D fan-beam CT of a patient treated by chemoradiotherapy for locally advanced non-small cell lung cancer, with the tumour and involved lymph nodes contoured on it (TCIA 4D-Lung).
- [4D-Lung, CBCT to CT](https://fidopt.io/dataset/Lung4D_CBCTCT_Syn/): The 50% breathing phase of a lung cancer patient's 4D cone-beam CT at a radiotherapy session (source), registered by the corpus onto the same phase of their 4D fan-beam CT (target), from TCIA 4D-Lung.
- [Lung-DIR-QA](https://fidopt.io/dataset/LungDIRQA/): Two chest CTs of one patient, with vessel bifurcations matched between them (Lung-DIR-QA).
- [Lung-PET-CT-Dx, CT to FDG-PET](https://fidopt.io/dataset/LungPETCTDx_CTPET_Syn/): CT (source) and FDG-PET in body-weight SUV (target) of one lung cancer patient's PET/CT session at the Second Affiliated Hospital of Harbin Medical University, the CT brought onto the PET grid through their shared scanner frame (Lung-PET-CT-Dx collection).
- [M4Raw, one 0.3 T T2 repetition to the mean of the others](https://fidopt.io/dataset/M4Raw_T2_Syn/): An axial T2-weighted brain MR of a healthy adult at 0.3 T: one acquisition as source and the mean of the same session's other repetitions of it as target (M4Raw).
- [M-CRIB 2.0 and M-CRIB-WM](https://fidopt.io/dataset/MCRIB/): Skull-stripped brain T2 MR of two healthy term neonates, with each brain's manual M-CRIB 2.0 parcellation (the ten brains of the M-CRIB atlases).
- [M-CRIB neonatal brain, 94 regions](https://fidopt.io/dataset/MCRIB_Seg/): T2 MR of the brain of one term neonate with the manual M-CRIB 2.0 parcellation of 94 regions.
- [MCT-LTDiag](https://fidopt.io/dataset/MCTLTDiag/): The portal venous CT of a patient with a liver tumour of one of five kinds (hepatocellular carcinoma, intrahepatic cholangiocarcinoma, colorectal or breast cancer metastases, haemangioma), every liver tumour segmented on it (MCT-LTDiag, Peking Union Medical College Hospital).
- [MCT-LTDiag, non-contrast to portal venous CT](https://fidopt.io/dataset/MCTLTDiag_Syn/): The non-contrast CT (source) and the portal venous CT (target) of one four-phase liver examination of a patient with a liver tumour, the first registered onto the second by the provider (MCT-LTDiag, Peking Union Medical College Hospital).
- [MMOTU CEUS, ovarian tumours in contrast-enhanced ultrasound](https://fidopt.io/dataset/MMOTU_CEUS/): A contrast-enhanced ultrasound image of an ovarian tumour, 2D and in colour, with the tumour outlined by a gynaecology expert and checked by a second (MMOTU's OTU_CEUS subset, Beijing Shijitan Hospital).
- [Paired 3T-7T brain MRI (UNC), 3T T1w to 7T T1w](https://fidopt.io/dataset/MR3T7T_Syn/): T1-weighted MR of one healthy adult's head at 3 T (source, MPRAGE) and 7 T (target, MP2RAGE), the 7T image brought onto the 3T grid by the provider's FSL FLIRT matrix (UNC paired 3T-7T dataset).
- [MR-ART (OpenNeuro ds004173), motion-corrupted T1w to still T1w](https://fidopt.io/dataset/MRART_Syn/): A motion-corrupted T1-weighted brain MRI (headmotion2) and a still T1-weighted scan of the same session, rigidly registered onto it by the corpus as the target (MR-ART, OpenNeuro ds004173).
- [MRBrainS18](https://fidopt.io/dataset/MRBrainS18/): Brain MR of an adult over 50 (diabetes, dementia or Alzheimer's disease, or a control with raised cardiovascular risk), T1, T1 inversion recovery and FLAIR aligned as one three-channel image, eight brain structures segmented by hand (MRBrainS18, UMC Utrecht).
- [MSD Colon](https://fidopt.io/dataset/MSD_Colon/): Portal venous CT of the abdomen of a patient before the resection of a primary colon cancer at Memorial Sloan Kettering Cancer Center, with the tumour segmented (Medical Segmentation Decathlon, Task10 Colon).
- [MSD Hepatic Vessel](https://fidopt.io/dataset/MSD_HepaticVessel/): Portal venous CT of the liver of a Memorial Sloan Kettering patient with a primary or metastatic liver tumour, with the liver's vessels and tumours segmented (Medical Segmentation Decathlon, Task08 HepaticVessel).
- [MSD Liver](https://fidopt.io/dataset/MSD_Liver/): Contrast-enhanced CT of the abdomen of a patient with a primary liver tumour or liver metastases, from the LiTS challenge's clinical sites, with the liver and its tumours segmented (Medical Segmentation Decathlon, Task03 Liver).
- [MSD Lung](https://fidopt.io/dataset/MSD_Lung/): Thin-section chest CT of a patient with non-small cell lung cancer before surgery, from Stanford University, with the tumour segmented (Medical Segmentation Decathlon Task06, from TCIA's NSCLC Radiogenomics).
- [MSD Pancreas](https://fidopt.io/dataset/MSD_Pancreas/): Portal venous abdominal CT of a patient before resection of a pancreatic mass at Memorial Sloan Kettering Cancer Center, with the pancreas and the mass segmented (Medical Segmentation Decathlon, Task07 Pancreas).
- [MSD Prostate](https://fidopt.io/dataset/MSD_Prostate/): Multiparametric prostate MR from Radboud: the transverse T2 and the ADC map as one two-channel image, with the peripheral zone and the rest of the gland segmented (Medical Segmentation Decathlon, Task05).
- [MSD Spleen](https://fidopt.io/dataset/MSD_Spleen/): Portal venous abdominal CT of a patient treated by chemotherapy for liver metastases at Memorial Sloan Kettering Cancer Center, with the spleen segmented (Medical Segmentation Decathlon, Task09 Spleen).
- [MSLesSeg](https://fidopt.io/dataset/MSLesSeg/): Raw FLAIR MR of the brain of one patient with multiple sclerosis at the first two visits of the MSLesSeg training set, 0.1 to 3.2 years apart, each on its own grid as acquired.
- [Multiple sclerosis lesions, Baghdad Teaching Hospital](https://fidopt.io/dataset/MSLesionsBaghdad/): Brain FLAIR MR of a patient with multiple sclerosis, 2D slices 5 to 8 mm apart at 1.5 T, the lesions outlined by a radiology resident and corrected by two consultants (Muslim et al. 2022).
- [MS lesions, Ljubljana](https://fidopt.io/dataset/MSLesionsLjubljana/): Brain MR of a multiple sclerosis patient, T1, contrast-enhanced T1, T2 and FLAIR co-registered as one four-channel image, the white matter lesions outlined by a consensus of three raters (Laboratory of Imaging Technologies, University of Ljubljana).
- [MSLesSeg, multiple sclerosis lesions](https://fidopt.io/dataset/MSLesionsMR/): FLAIR MR of a multiple sclerosis patient's brain, registered to MNI152 at 1 mm and skull-stripped by the provider, every hyperintense lesion outlined by a junior rater and validated by two specialists (MSLesSeg, ICPR 2024).
- [MSU-PID](https://fidopt.io/dataset/MSUPID/): Chlorophyll fluorescence images of one Arabidopsis plant seen from above at 9 am on day 7 (fixed) and day 9 (moving), every leaf outlined and its two tips marked on both (MSU-PID, Michigan State University).
- [MU-Glioma-Post, glioma after treatment](https://fidopt.io/dataset/MUGliomaPostMR/): Post-treatment brain MR of a glioma patient at the University of Missouri: T1, post-contrast T1, T2 and FLAIR as one four-channel image on SRI24, skull-stripped, with BraTS 2024's four compartments labelled (MU-Glioma-Post, TCIA).
- [Mandibular CT Dataset Collection](https://fidopt.io/dataset/MandibleCT/): A head and neck CT of a patient treated in the oral and maxillofacial surgery department in Graz, with the mandible outlined slice by slice by a clinical expert (Mandibular CT Dataset Collection, Wallner and Egger 2018).
- [Brain/MINDS marmoset in vivo and ex vivo T2 MRI](https://fidopt.io/dataset/MarmosetInVivoExVivoMR/): The in vivo and the ex vivo, fixed, T2-weighted images of one marmoset, with the provider's 52 atlas regions a hemisphere on each.
- [Marmoset STPT, between-animal registration](https://fidopt.io/dataset/MarmosetSTPT/): Serial two-photon tomography brains of two marmosets from the Brain/MINDS Marmoset Connectivity Resource, at 0.1 mm, with 36 atlas-derived regional labels.
- [Mayo LDCT-and-Projection-data, low-dose to full-dose CT](https://fidopt.io/dataset/MayoLDCT_Syn/): Low-dose (source) and full-dose (target) reconstructions of one chest or abdomen CT, the low dose made by Mayo Clinic inserting noise into the same projections (TCIA LDCT-and-Projection-data, Siemens exams).
- [Mediastinal-Lymph-Node-SEG](https://fidopt.io/dataset/MediastinalLymphNodesCT/): Contrast-enhanced chest CT of a patient at the baseline of an oncology trial, every abnormal mediastinal lymph node delineated by hand (Mediastinal-Lymph-Node-SEG, the fully annotated scans of LNQ2023).
- [Micro-ultrasound prostate](https://fidopt.io/dataset/MicroUSProstate/): A transrectal micro-ultrasound sweep of the prostate before a biopsy: the frames of the probe's rotation stacked, the prostate outlined on each and reviewed by an expert urologist (Micro-Ultrasound Prostate Segmentation Dataset).
- [Middlebury optical flow](https://fidopt.io/dataset/MiddleburyFlow/): Two colour frames of one scene a moment apart, real, rendered or a stereo pair: frame 10 (fixed) and frame 11 (moving) of a Middlebury optical flow sequence with public ground truth.
- [Mindboggle-101](https://fidopt.io/dataset/Mindboggle101/): Skull-stripped brain T1 MR scans of two healthy adults from Mindboggle-101 release 3, with 62 cortical regions labelled by hand on both.
- [Mindboggle-101, 62 cortical regions](https://fidopt.io/dataset/Mindboggle101_Seg/): T1 MR of the brain of one healthy adult, skull-stripped, with the 62 cortical regions of the DKT31 protocol labelled by hand (Mindboggle-101).
- [MiniVess, rodent cortical microvessels](https://fidopt.io/dataset/MiniVess/): An in vivo multiphoton fluorescence volume of rodent cortical blood vessels, with a binary vessel mask made by an automated pipeline and proofread by hand.
- [MitoNet TEM benchmark](https://fidopt.io/dataset/MitoNetTEM/): A 2D transmission electron micrograph of cells or tissue, its mitochondria segmented by hand: one of the 100 TEM benchmark images MitoNet's authors kept out of their training data (EMPIAR-10982).
- [Monash vis-fPET-fMRI (OpenNeuro ds003382), T1w to FDG-PET](https://fidopt.io/dataset/MonashPETMR_Syn/): One simultaneous PET/MR session of a healthy adult under a constant FDG infusion: the T1w MPRAGE (source) and the static FDG-PET in Bq/mL (target), on the T1w's grid after a rigid motion correction (OpenNeuro ds003382).
- [Montgomery County chest X-rays, lungs and heart](https://fidopt.io/dataset/MontgomeryCXR/): A frontal chest radiograph from Montgomery County's tuberculosis screening, 2D, its lungs drawn under a radiologist's supervision (National Library of Medicine) and its heart drawn by researchers and reviewed by a clinician (PhysioNet).
- [MMB-MRI](https://fidopt.io/dataset/MouseBrainMR/): T2-weighted MR at 11.7 T of the skull-stripped brains of two C57BL/6J mice, with 50 regions labelled (MMB-MRI, the 47 mice whose labels were corrected by hand).
- [Mouse whole-body CT and MRI](https://fidopt.io/dataset/MouseCTMR/): Micro-CT (fixed) and 7 T MRI (moving) of one mouse, scanned one after the other in one animal holder 4.5 hours after an injection (Preclinical CT and MRI liver imaging dataset, Aachen).
- [BBBC050, nuclei of mouse embryonic cells](https://fidopt.io/dataset/MouseEmbryoNuclei/): A three-dimensional fluorescence volume of an early mouse embryo at one annotated time point, its manually annotated nuclei merged into one foreground label (BBBC050).
- [Mouse whole-body micro-CT](https://fidopt.io/dataset/MouseMicroCT/): Whole-body micro-CT of one mouse at its first and its last time point, anaesthetised and positioned anew in between, with its organs labelled on both (Rosenhain et al., preclinical micro-CT database).
- [Mouse whole-body micro-CT, ten organs](https://fidopt.io/dataset/MouseMicroCT_Seg/): Whole-body micro-CT of one mouse with ten organs segmented: the fixed images of MouseMicroCT's pairs.
- [Multimodal-HC, whole-body MR/CT](https://fidopt.io/dataset/MultimodalHC_MRCT/): Low-dose CT (fixed) and Dixon in-phase MR (moving) of the whole body, vertex to mid-femur, of one healthy adult on two scanners in two rooms (Multimodal-HC, Rigshospitalet).
- [Multimodal-HC, whole-body MR to CT](https://fidopt.io/dataset/MultimodalHC_MRCT_Syn/): Whole-body Dixon in-phase MR (source) and low-dose CT (target) of one healthy adult, from the vertex to mid-femur, on two scanners in two rooms, the MR registered onto the CT by the corpus (Multimodal-HC, Rigshospitalet).
- [Multimodal-HC, NAC PET to CT](https://fidopt.io/dataset/MultimodalHC_PETCT_Syn/): FDG PET without attenuation correction (source) and the low-dose CT reconstructed for its attenuation correction (target), from the vertex to mid-femur, of one healthy adult's PET/CT session on a total-body scanner (Multimodal-HC, Rigshospitalet).
- [Spinal-Multiple-Myeloma-SEG, vertebrae and lytic lesions](https://fidopt.io/dataset/MyelomaSpineCT/): The conventional CT of a dual-layer low-dose scan of a patient with multiple myeloma, cropped to the spine, each vertebra from C1 to L5 and the spine's lytic lesions segmented (Spinal-Multiple-Myeloma-SEG, TCIA).
- [Spinal-Multiple-Myeloma-SEG, conventional CT to 40 keV monoenergetic image](https://fidopt.io/dataset/MyelomaSpineDECT_Syn/): Conventional CT (source) and 40 keV virtual monoenergetic image (target) of one low-dose dual-layer scan of a patient with multiple myeloma, cropped to the spine: two reconstructions of one acquisition on one grid (Spinal-Multiple-Myeloma-SEG, TCIA).
- [MyoSegmenTUM thigh muscles](https://fidopt.io/dataset/MyoSegmenTUM/): Water image of a chemical-shift-encoded MR of both thighs, the stack nearest the hip, of a healthy volunteer or a patient with a neuromuscular disease, with four muscle groups of each thigh drawn by hand and checked by a radiologist (MyoSegmenTUM_thigh).
- [Myocardial perfusion SPECT](https://fidopt.io/dataset/MyocardialSPECT/): Rest myocardial perfusion SPECT (99mTc-MIBI) of two patients, each with the dataset's mask of the left ventricular wall (Myocardial perfusion scintigraphy image database, PhysioNet), paired by us.
- [NFBS brain masks](https://fidopt.io/dataset/NFBSBrainMask/): Defaced T1-weighted MR of one adult of the Enhanced Nathan Kline Institute Rockland Sample's neurofeedback study, with its brain mask from BEaST checked by eye and edited by hand where needed (Neurofeedback Skull-stripped repository).
- [NLST, sharp-kernel CT to soft-kernel CT](https://fidopt.io/dataset/NLSTKernel_Syn/): Two reconstructions of one low-dose chest CT acquisition from the National Lung Screening Trial: a sharp kernel (source: Siemens B50f, GE LUNG or BONE) and the maker's soft kernel (target: Siemens B30f, GE STANDARD).
- [LIDC-annot-NLST501](https://fidopt.io/dataset/NLSTNodules/): Low-dose chest CT of a National Lung Screening Trial participant, with the lung nodules and masses that at least two of four independent radiologists segmented (LIDC-annot-NLST501, a TCIA analysis result of 2026).
- [NLSTseg](https://fidopt.io/dataset/NLSTSeg/): Low-dose CT of a National Lung Screening Trial participant diagnosed with lung cancer, from the screening year of the diagnosis, with the cancer and any suspicious nodule beside it painted by hand (NLSTseg).
- [NSCLC-Radiomics-Interobserver1](https://fidopt.io/dataset/NSCLCInterobserver/): The pretreatment CT of a patient with non-small cell lung cancer treated by radiotherapy at MAASTRO, with the primary tumour where at least three of five radiation oncologists, outlining it blind and by hand, placed it (NSCLC-Radiomics-Interobserver1, TCIA version 3).
- [NSCLC Radiogenomics, CT to FDG-PET](https://fidopt.io/dataset/NSCLCRadiogenomics_CTPET_Syn/): CT (source) and FDG-PET in body-weight SUV (target) of one patient's PET/CT session, the CT brought onto the PET grid through their shared scanner frame (NSCLC Radiogenomics collection).
- [NSCLC-Radiomics, Lung1](https://fidopt.io/dataset/NSCLCRadiomicsGTV/): The pretreatment CT of a patient with non-small cell lung cancer treated by radiotherapy at MAASTRO, with the primary tumour's gross volume outlined by a radiation oncologist (NSCLC-Radiomics, Lung1, TCIA version 4).
- [NaF PROSTATE PET-CT, CT to sodium fluoride PET](https://fidopt.io/dataset/NaFProstate_CTPET_Syn/): Low-dose CT (source) and 18F-sodium fluoride bone PET in body-weight SUV (target) of one prostate cancer patient's PET/CT session on a Philips Gemini TF, the CT brought onto the PET grid through their shared scanner frame (NaF PROSTATE collection).
- [MRM NeAt mouse brain atlas](https://fidopt.io/dataset/NeAtMouseBrainMR/): T2-weighted MR of the head of an adult male C57BL/6J mouse at 9.4 T, alive, with 20 brain structures labelled a side (MRM NeAt in vivo atlas, Ma et al. 2008, as re-oriented by Ma at UCL).
- [BONBID-HIE neonatal lesions](https://fidopt.io/dataset/NeonatalHIEMR/): Skull-stripped ADC map of the brain of a term neonate with hypoxic-ischaemic encephalopathy, the injured tissue outlined by experts (BONBID-HIE, Massachusetts General Hospital).
- [NeuroPAL atlas (C. elegans heads)](https://fidopt.io/dataset/NeuroPAL/): Confocal fluorescence volume of the head of two young-adult C. elegans hermaphrodites, the panneuronal TagRFP-T channel of NeuroPAL, paired by us from the ten worms of the NeuroPAL atlas (DANDI 000715).
- [NuInsSeg, nuclei outlined by hand on H&E](https://fidopt.io/dataset/NuInsSeg/): A 512-pixel H&E patch of one whole slide of a human or mouse organ, every nucleus outlined by hand and the areas too ambiguous to outline marked apart (NuInsSeg, Medical University of Vienna).
- [ON-Harmony (OpenNeuro ds004712), Siemens T1w to Philips T1w](https://fidopt.io/dataset/ONHarmony_Syn/): T1-weighted brain MR of one healthy adult on a Siemens Prisma in Oxford (source) and on a Philips Ingenia in Nottingham on another visit (target), the target rigidly registered onto the source by the corpus (ON-Harmony travelling heads).
- [OpenEar, inter-specimen temporal-bone CBCT](https://fidopt.io/dataset/OpenEar/): A pair of distinct cadaver temporal bones, CBCT to CBCT, scored on the nine small middle- and inner-ear structures both specimens hold whole, drawn by the provider (OpenEar).
- [OpenEar, temporal-bone CBCT segmentation](https://fidopt.io/dataset/OpenEar_Seg/): Registered CBCT of one post-mortem temporal-bone specimen from the OpenEar surgical simulation library, with thirteen structures delineated on the co-registered CBCT and micro-slicing images.
- [OpenKBP](https://fidopt.io/dataset/OpenKBP/): Head and neck radiotherapy planning CTs of two patients, downsampled to 128 x 128 x 128 voxels by the OpenKBP challenge, with the organs at risk the clinics contoured on both, paired by us.
- [OpenOrganelle ground-truth crops](https://fidopt.io/dataset/OpenOrganelleEM/): A block of a FIB-SEM volume of cultured cells or mouse or fly tissue, 2 to 8 nm a voxel, every voxel labelled by hand by Janelia's annotators, merged into twelve structures (OpenOrganelle).
- [Optical to SAR (SpaceNet 9, BRIGHT)](https://fidopt.io/dataset/OpticalSAR/): Optical (fixed) and radar (SAR, moving) satellite images of one town after an earthquake, explosion or eruption, at 0.3 to 0.45 m a pixel, with point pairs placed by people on the ground.
- [ORION colorectal cancer, H&E and Hoechst of one section, known warp](https://fidopt.io/dataset/OrionCRC/): A 2048-pixel square (0.67 mm) of one colorectal cancer section: its H&E (fixed, colour) and its Hoechst channel imaged before staining (moving), deformed by a known smooth warp (ORION study, Nature Cancer 2023).
- [ORION colorectal cancer, H&E to Hoechst of one section](https://fidopt.io/dataset/OrionCRC_HEIF_Syn/): A 2048-pixel square of one colorectal cancer section at 0.325 µm a pixel: its H&E (source) and the Hoechst channel of the immunofluorescence image taken before staining (target), from the ORION study (Nature Cancer 2023).
- [PANORAMA](https://fidopt.io/dataset/PANORAMA/): Contrast-enhanced CT of the upper abdomen of one patient with pancreatic ductal adenocarcinoma, from Radboud University Medical Center or University Medical Center Groningen, the tumour drawn by hand (PANORAMA's public set).
- [TSPO PET/MR in chronic pain (MGH, OpenNeuro ds007907), T1w to [11C]PBR28 PET](https://fidopt.io/dataset/PBR28_MRPET_Syn/): T1-weighted MR of the head (source) and the static [11C]PBR28 PET of minutes 60 to 90 in SUV (target) of one PET/MR session, the T1w resampled onto the PET grid by the provider (OpenNeuro ds007907).
- [PDDCA](https://fidopt.io/dataset/PDDCA/): Head and neck CT of two patients treated by radiotherapy for stage III or IV cancer of the oropharynx, hypopharynx or larynx, paired by us from PDDCA 1.4.1 (RTOG 0522 trial; MICCAI 2015 challenge).
- [PDDCA, head and neck organs at risk](https://fidopt.io/dataset/PDDCA_Seg/): Head and neck CT of one patient treated by radiotherapy, with nine organs at risk contoured by hand (PDDCA, MICCAI 2015).
- [PENGWIN CT](https://fidopt.io/dataset/PENGWIN/): Pelvic CT of a patient with a pelvic fracture before reduction surgery, from six medical centres in China, with the sacrum and the two hip bones labelled (PENGWIN 2024 challenge, task 1).
- [PENGWIN 2026, femur](https://fidopt.io/dataset/PENGWIN2026_Femur/): CT of one side of the hips and thighs of a patient with a femoral fracture before surgery, from seven Chinese hospitals, with the broken femur labelled (PENGWIN 2026 challenge, tasks 1 and 2, femur part).
- [PFUS1, the pelvic floor on transperineal ultrasound](https://fidopt.io/dataset/PFUS/): The first frame of a transperineal ultrasound video of a woman's pelvic floor in the midsagittal plane, at rest, with eight structures outlined as polygons by sonographers under an expert: one woman of PFUS1 (Valme University Hospital, Seville, 2023).
- [PI-CAI prostate cancer lesions](https://fidopt.io/dataset/PICAI/): Biparametric prostate MR from one of three Dutch centres: T2, ADC and high b-value diffusion as three channels on the T2's grid, with the clinically significant cancers drawn by people (PI-CAI).
- [POPI](https://fidopt.io/dataset/POPI/): 4D chest CT, two respiratory phases of one patient (POPI model).
- [PROMISE12](https://fidopt.io/dataset/PROMISE12/): Prostate T2 MR of two patients of one centre, from the PROMISE12 challenge's test and live-challenge cases, paired by us, with the prostate segmented on both.
- [PROMISE12, prostate](https://fidopt.io/dataset/PROMISE12_Seg/): T2 MR of one patient's prostate, with the challenge's reference segmentation of the gland (PROMISE12).
- [PROSTATEx gland zones](https://fidopt.io/dataset/PROSTATEx_Seg/): Transverse T2 MR of the prostate of one man examined for prostate cancer at 3 T without an endorectal coil, the peripheral zone and the rest of the gland drawn by radiologists (PROSTATEx masks).
- [PSMA-PET-CT-Lesions follow-up (Learn2Reg 2026 PSMAReg)](https://fidopt.io/dataset/PSMAFollowUp/): Whole-body CT of one man with prostate cancer at his first PSMA-PET/CT study (fixed) and his second, 98 to 171 days later (moving), PSMA-avid lesions drawn on each PET (PSMA-PET-CT-Lesions; Learn2Reg 2026 PSMAReg).
- [PSMA-PET-CT-Lesions (autoPET III and IV), PET lesions](https://fidopt.io/dataset/PSMALesionsPET/): Whole-body PSMA-PET in SUV of a man with suspected or diagnosed prostate cancer, every PSMA-avid tumour lesion segmented on the PET by one reader and validated by board-certified experts (PSMA-PET-CT-Lesions, autoPET III and IV).
- [Paired head CT and MR, MR to CT](https://fidopt.io/dataset/PairedHeadMRCT_Syn/): Contrast-enhanced T1-weighted MR of the head of a patient before neurosurgery and the thin-slice CT to synthesise from it, both put on one 0.5 mm grid by the provider (A Paired Head CT-MRI Dataset for Cross-Modality Image Synthesis, The First Affiliated Hospital, Sun Yat-sen University).
- [PanTrack](https://fidopt.io/dataset/PanTrack/): Two consecutive portal venous CTs of a patient under treatment for pancreatic adenocarcinoma, the earlier fixed, with the lesions a radiologist segmented and linked between them (PanTrack, one German institution).
- [PanTrack](https://fidopt.io/dataset/PanTrackCT/): The first portal venous CT of a patient's follow-up for pancreatic adenocarcinoma, with the pancreatic tumour a radiologist segmented on it (PanTrack, one German institution).
- [Pancreas-CT, 8 organs](https://fidopt.io/dataset/PancreasCT8/): Contrast-enhanced abdominal CT of two patients of the NIH Clinical Center in the portal-venous phase (Pancreas-CT), with eight organs labelled by Gibson et al., paired by us.
- [Pancreas-CT, 8 organs](https://fidopt.io/dataset/PancreasCT8_Seg/): Portal venous abdominal CT of one person with Gibson et al.'s reference segmentations of eight organs (NIH Pancreas-CT).
- [PanSegData, pancreas on T2-weighted MR](https://fidopt.io/dataset/PancreasMR/): A T2-weighted abdominal MR of a participant referred for a pancreatic cyst or a suspected pancreatic cancer at one of five US centres, with the pancreas outlined by a radiologist (PanSegData).
- [Pancreatic-CT-CBCT-SEG](https://fidopt.io/dataset/PancreaticCTCBCT/): Breath-hold planning CT (fixed) and cone-beam CT (moving) of one patient treated by radiotherapy for pancreatic cancer (Pancreatic-CT-CBCT-SEG).
- [Pancreatic-CT-CBCT-SEG, bowel on the cone-beam CT](https://fidopt.io/dataset/PancreaticCTCBCT_SegCBCT/): Breath-hold cone-beam CT of one patient treated for pancreatic cancer, with the stomach and duodenum and the small bowel contoured by radiation oncologists.
- [Pancreatic-CT-CBCT-SEG, bowel on the planning CT](https://fidopt.io/dataset/PancreaticCTCBCT_SegCT/): Breath-hold planning CT of one patient treated for pancreatic cancer, with the stomach and duodenum and the small bowel contoured by radiation oncologists.
- [Pediatric-CT-SEG](https://fidopt.io/dataset/PediatricCT/): Chest-abdomen-pelvis or abdomen-pelvis CT of two children of one sex and about one age, from three scanners of one hospital, with up to 28 structures contoured (Pediatric-CT-SEG), paired by us.
- [Pediatric-CT-SEG, organs of children](https://fidopt.io/dataset/PediatricCT_Seg/): Chest, abdomen and pelvis CT of one child with up to 28 structures contoured (Pediatric-CT-SEG).
- [Pediatric thoracic dynamic MRI](https://fidopt.io/dataset/PediatricThoraxMR/): Free-breathing dynamic MRI of one healthy child's thorax and upper abdomen, the end-expiration (fixed) and end-inspiration (moving) volumes of one 4D image, lungs, liver, spleen and kidneys segmented at both (Virtual Growing Child).
- [Pediatric thoracic dynamic MRI, six organs](https://fidopt.io/dataset/PediatricThoraxMR_Seg/): Dynamic MR of one healthy child's thorax and upper abdomen, at end expiration or end inspiration, with the lungs, liver, spleen and kidneys segmented.
- [Pelvic-Reference-Data](https://fidopt.io/dataset/PelvicReference/): Treatment CBCT (fixed) and planning CT (moving) of the pelvis of one radiotherapy patient, 4 to 20 days apart (Pelvic-Reference-Data).
- [Pelvic-Reference-Data, CBCT to CT](https://fidopt.io/dataset/PelvicReference_Syn/): Treatment cone-beam CT (source) and planning CT (target) of the pelvis of one radiotherapy patient, 4 to 40 days apart, the CBCT registered onto the CT by the corpus (Pelvic-Reference-Data).
- [Pelvic landmarks CT/CT (LUMC)](https://fidopt.io/dataset/PelvisLandmarksCT/): Two planning CTs of one cervical cancer patient's pelvis, full bladder (fixed) and empty bladder (moving), with corresponding landmarks placed by people on both (LUMC interobserver study of landmark placement).
- [Pelvic landmarks MR/CT (LUMC)](https://fidopt.io/dataset/PelvisLandmarksMRCT/): T2-weighted pelvic MR of a cervical cancer patient with a brachytherapy applicator in place (fixed) and her CT seven weeks earlier (moving), with landmarks placed by people on both (LUMC interobserver study).
- [TotalSegmentator pleural_pericard_effusion, pericardial effusion](https://fidopt.io/dataset/PericardialEffusionCT/): Chest CT of a patient with a pericardial effusion or haemopericardium at the University Hospital Basel, the effusion drawn by hand by a radiology resident under a cardiothoracic radiologist (Wilder-Smith et al. 2022).
- [Cardiac CT of growing pigs (A heart for pigs)](https://fidopt.io/dataset/PigCardiacCT/): Contrast-enhanced ECG-gated cardiac CT of one growing pig at two consecutive scanning rounds, the first phase of the later (fixed) and the earlier (moving), the heart and left ventricle drawn on both (Norsvin, NMBU, NTNU).
- [Cardiac CT of pigs, heart and left ventricle](https://fidopt.io/dataset/PigCardiacCT_Seg/): Contrast-enhanced ECG-gated cardiac CT of one growing pig, the first phase of the 4D scan, with the heart and its left ventricular cavity drawn by hand.
- [Cardiac cine MR of pigs at 7 T (cmr-cine-sscrofa)](https://fidopt.io/dataset/PigCardiacMR/): Short-axis cine MR of one pig's heart at 7 T, end diastole (fixed) and end systole (moving), 12 days after an infarction or a sham procedure, the left ventricular cavity and myocardium drawn at both.
- [Cine MR of pigs at 7 T, left ventricle](https://fidopt.io/dataset/PigCardiacMR_Seg/): Short-axis cine MR stack of one pig's heart at 7 T, at end diastole or end systole, 12 days after a myocardial infarction or sham procedure, the left ventricular cavity and myocardium drawn by hand.
- [Pituitary neuroendocrine tumour MRI](https://fidopt.io/dataset/PituitaryTumourMR/): Contrast-enhanced T1 MR of a patient before surgery for a pituitary neuroendocrine tumour (adenoma), the tumour and both internal carotid arteries segmented semi-automatically by neurosurgical residents and checked by experts (Pandit et al. 2025).
- [PleThora](https://fidopt.io/dataset/PleThoraCT/): Pretreatment chest CT of a patient with non-small cell lung cancer and a pleural effusion, treated at MAASTRO Clinic (TCIA's NSCLC-Radiomics), with the left and right thoracic cavities and the effusion segmented (PleThora).
- [Prostate158 zones](https://fidopt.io/dataset/Prostate158/): Biparametric 3 T prostate MR of one patient at Charité Berlin, the T2, ADC and DWI as one three-channel image on the T2's grid, with the transitional and peripheral zones drawn by a radiologist (Prostate158, test split).
- [Prostate-Anatomical-Edge-Cases](https://fidopt.io/dataset/ProstateEdgeCasesCT/): Radiotherapy simulation CT of the pelvis of a man with prostate cancer, most with an anatomical variant chosen to stress autosegmentation, the prostate, bladder, rectum and femoral heads contoured by one radiation oncologist (Prostate-Anatomical-Edge-Cases).
- [NCI-ISBI 2013 prostate](https://fidopt.io/dataset/ProstateISBI2013/): Transverse T2 MR of one patient's prostate, at 3 T without an endorectal coil (Radboud) or at 1.5 T with one (Boston Medical Center), its central gland and peripheral zone outlined by experts (NCI-ISBI 2013).
- [Prostate-MRI-US-Biopsy](https://fidopt.io/dataset/ProstateMRUS/): T2 MR (fixed) and 3D transrectal ultrasound (moving) of one patient's prostate, the MR before an MR-ultrasound fusion biopsy and the ultrasound at its start (Prostate-MRI-US-Biopsy, UCLA).
- [Prostate-MRI-US-Biopsy, the gland on MR](https://fidopt.io/dataset/ProstateMRUS_Seg/): T2 MR of the prostate of one patient before a fusion biopsy, with the gland contoured semi-automatically.
- [LCTSC CT and simulated CBCT, known deformation](https://fidopt.io/dataset/PsCBCTThorax/): Planning CT of the thorax (fixed, Hounsfield units) and the CBCT simulated from it (moving, normalised, no unit), deformed by a known transform the corpus adds (LCTSC through Zenodo 5035494).
- [Simulated thoracic CBCT, four clinical contours](https://fidopt.io/dataset/PsCBCTThorax_Seg/): Simulated CBCT of the thorax (normalised, no unit) with the clinical contours of the spinal cord, oesophagus, heart and lungs of the planning CT it was simulated from.
- [Simulated CBCT to planning CT, LCTSC](https://fidopt.io/dataset/PsCBCTThorax_Syn/): Simulated CBCT (normalised, no unit) as source and the planning CT it was simulated from, in Hounsfield units, as target on the same cropped grid.
- [QIN-BREAST, prone CT to PET](https://fidopt.io/dataset/QINBreast_CTPET_Syn/): Low-dose CT (source) and FDG-PET in SUV (target) of the chest of a woman with breast cancer lying prone, from one PET/CT session before or during neoadjuvant chemotherapy, the CT on the PET's grid (QIN-BREAST).
- [QIN-PROSTATE-Repeatability](https://fidopt.io/dataset/QINProstateRepeat/): Prostate T2 MR of one patient at two exams within two weeks, on the same scanner with an endorectal coil (QIN-PROSTATE-Repeatability, test and retest).
- [QIN-PROSTATE-Repeatability, zones](https://fidopt.io/dataset/QINProstateRepeat_Seg/): T2 MR of the prostate of one patient, with the gland and its peripheral zone contoured by a radiologist.
- [QUADRA_HC, whole-body CT test-retest](https://fidopt.io/dataset/QuadraHC/): Low-dose whole-body CT, vertex to thighs, of one healthy adult scanned twice on one PET/CT scanner weeks apart: first session fixed, second moving (QUADRA_HC, Medical University of Vienna).
- [3D-RCAN confocal to STED, nuclei stained with SiR-DNA](https://fidopt.io/dataset/RCANConfocalSTED_Syn/): A confocal volume taken at low excitation (source) and the STED volume (target) of one field of fixed mouse embryonic fibroblasts stained with SiR-DNA, on one microscope (3D-RCAN, Chen et al., Nature Methods 2021).
- [RCC-AID](https://fidopt.io/dataset/RCCAID/): Contrast-enhanced abdominal CT of a patient with a clear cell, papillary or chromophobe renal cell carcinoma (TCGA-KIRC, TCGA-KIRP, TCGA-KICH), kidneys, masses and cysts segmented by a model and corrected by students (RCC-AID).
- [READ-PE pulmonary emboli](https://fidopt.io/dataset/READPE/): CT pulmonary angiography of one patient with acute pulmonary embolism, on a GE or Toshiba scanner, with the emboli drawn by a radiology resident and revised by a radiologist (READ-PE).
- [RESECT](https://fidopt.io/dataset/RESECT/): Intra-operative ultrasound before resection (fixed) and pre-operative FLAIR MR (moving) of one patient with a low-grade glioma (RESECT, the data of the CuRIOUS challenges).
- [RHPE hand radiographs](https://fidopt.io/dataset/RHPE/): Radiographs of both hands of two children of the Fundación Santa Fe de Bogotá, with 17 keypoints on the fingers and wrist of the left-hand side of the image placed by trained annotators on each (Radiological Hand Pose Estimation, test split).
- [RHUH-GBM, glioblastoma before surgery](https://fidopt.io/dataset/RHUHGlioblastomaMR/): Pre-operative brain MR of a patient with a glioblastoma later totally or near totally resected at Río Hortega University Hospital, Valladolid: T1, post-contrast T1, T2 and FLAIR as one four-channel image on SRI24, skull-stripped, with necrosis, oedema and enhancing tumour labelled (RHUH-GBM, TCIA).
- [MIDRC-RICORD-1A](https://fidopt.io/dataset/RICORD1aCOVIDCT/): One chest CT of an adult with COVID-19, from four sites in four countries, with the infectious opacities outlined slice by slice by a thoracic radiologist (MIDRC-RICORD-1A, RSNA and the Society of Thoracic Radiology).
- [RIDER Lung CT](https://fidopt.io/dataset/RIDERLungCT/): Chest CT of one patient with non-small cell lung cancer, scanned twice within 15 minutes on the same scanner, with the primary tumour drawn by hand on both (RIDER Lung CT, test and retest).
- [RIDER Lung CT, primary tumour](https://fidopt.io/dataset/RIDERLungCT_Seg/): Chest CT of one patient with non-small cell lung cancer, with the primary tumour drawn by hand by a radiation oncologist (RIDER-LungCT-Seg).
- [RIDER Lung PET-CT, CT to FDG-PET](https://fidopt.io/dataset/RIDERLung_CTPET_Syn/): CT (source) and FDG-PET in body-weight SUV (target) of one lung cancer patient's PET/CT session on a GE Discovery STE, the CT brought onto the PET grid through their shared scanner frame (RIDER Lung PET-CT collection).
- [ReMIND, brain tumour before resection](https://fidopt.io/dataset/ReMINDTumourMR/): Pre-operative head MR of an adult about to have a brain tumour resected at Brigham and Women's Hospital: the one defaced series the surgical team outlined the tumour on, with that whole-tumour outline (ReMIND, TCIA).
- [RibFrac](https://fidopt.io/dataset/RibFracCT/): A chest-abdomen CT of a patient with rib fractures at Huadong Hospital, Shanghai, with every fracture outlined as a region (RibFrac challenge, training and tuning sets).
- [RibSeg v2](https://fidopt.io/dataset/RibSeg/): Chest-abdomen CT of two patients from one hospital, most with rib fractures (RibFrac), their 24 ribs labelled one by one (RibSeg v2), paired by us.
- [RibSeg v2, individual ribs](https://fidopt.io/dataset/RibSeg_Seg/): A native chest-abdomen CT with its 24 ribs numbered one by one (RibSeg v2): the fixed images of RibSeg's registration pairs.
- [SAROS body regions](https://fidopt.io/dataset/SAROSBodyCT/): CT of the abdomen, chest or whole body from an open TCIA collection, resampled to 5 mm slices, with 13 body regions corrected by people on every fifth slice (SAROS, University Hospital Essen).
- [SELMA3D c-Fos-positive cells, light-sheet microscopy](https://fidopt.io/dataset/SELMA3D_CFos/): A 100 x 100 x 100 voxel patch of a light-sheet volume of a cleared mouse brain, its c-Fos-positive cells drawn by experts (SELMA3D 2024).
- [SELMA3D cell nuclei of the human brain, light-sheet microscopy](https://fidopt.io/dataset/SELMA3D_Nuclei/): A 200 x 200 x 200 voxel patch of a light-sheet volume of cleared human brain tissue, its cell nuclei drawn by experts (SELMA3D 2024).
- [SELMA3D amyloid plaques, light-sheet microscopy](https://fidopt.io/dataset/SELMA3D_Plaques/): A 300 x 300 x 300 voxel patch of a light-sheet volume of a cleared 5xFAD mouse brain, its amyloid plaques drawn by experts (SELMA3D 2024).
- [SELMA3D blood vessels (VesSAP), light-sheet microscopy](https://fidopt.io/dataset/SELMA3D_Vessels/): A 500 x 500 x 50 voxel patch of a light-sheet volume of a cleared mouse brain, its blood vessels drawn by experts (SELMA3D 2024, patches from VesSAP).
- [SHG/BF TMA cores (Eliceiri)](https://fidopt.io/dataset/SHGBF/): A second-harmonic generation image (SHG, fixed) and a bright-field image (moving) of one H&E-stained breast carcinoma tissue microarray core, the central 834 x 834 px patch, the bright-field deformed by a known smooth transform.
- [SNEMI3D sections, known in-plane deformation](https://fidopt.io/dataset/SNEMI3D/): A mouse cortex serial-section electron microscopy image paired with a known smooth deformation of itself: it measures the recovery of a known in-plane warp, not the alignment of adjacent sections.
- [SOOP acute stroke lesions](https://fidopt.io/dataset/SOOPStroke/): Brain diffusion MR of a patient admitted with an acute ischaemic stroke: the b=1000 trace image and the ADC map as one two-channel image, the acute lesion traced by hand (SOOP, OpenNeuro ds004889).
- [SPIDER](https://fidopt.io/dataset/SPIDER/): Sagittal T1 (fixed) and T2 (moving) MR of the lumbar spine from one study of a patient with low back pain, the T2 deformed by a known smooth transform (SPIDER).
- [SPIDER, lumbar vertebrae, discs and canal](https://fidopt.io/dataset/SPIDER_Seg/): Sagittal T1 MR of the lumbar spine of one patient with low back pain, with each vertebra, intervertebral disc and the spinal canal labelled.
- [STACOM 2011 cardiac motion](https://fidopt.io/dataset/STACOM2011/): 3D tagged MR of the heart of a healthy volunteer at end diastole (fixed) and end systole (moving) of one cycle (STACOM 2011 cardiac motion analysis challenge).
- [STARE, retinal vessels drawn by hand](https://fidopt.io/dataset/STARE/): A colour photograph of the retina, 2D, with its blood vessels drawn by hand: one of the twenty images of the STARE project's vessel segmentation set (Hoover, Kouznetsova and Goldbaum 2000), nine normal, eleven diseased.
- [STRAUS 3D synthetic echocardiography](https://fidopt.io/dataset/STRAUS3DEcho/): B-mode frames 0 and 10 of one simulated 3D echocardiographic sequence, one cardiac activation scenario, with the simulation's myocardial mesh vertices paired between the two frames (STRAUS).
- [SUN3D](https://fidopt.io/dataset/SUN3D/): Two colour frames of a hand-held RGB-D video of one indoor place, half a second apart: images m (fixed) and m + 15 (moving) at the middle of a SUN3D sequence.
- [Soft-tissue-Sarcoma](https://fidopt.io/dataset/SarcomaLimbMR/): T2-weighted fat-saturated or STIR MR of a soft-tissue sarcoma of the extremities before treatment, the tumour and any visible oedema around it drawn slice by slice by an expert radiation oncologist (Soft-tissue-Sarcoma, TCIA).
- [Spine-generic multi-subject](https://fidopt.io/dataset/SpineGeneric/): Sagittal 3D T2w MR of the cervical spine of two adults scanned on one scanner with the spine-generic protocol, paired by us (spine-generic multi-subject, release r20250310).
- [Spine-generic, spinal cord](https://fidopt.io/dataset/SpineGeneric_Seg/): Sagittal 3D T2-weighted MR of the cervical spine of one adult, with the spinal cord segmented by a network and corrected by hand.
- [Spine-Mets-CT-SEG](https://fidopt.io/dataset/SpineMetsCT/): Radiotherapy simulation CT of a patient with spinal metastases at Brigham and Women's Hospital, each vertebra from T1 to L5 segmented in the annotated slices (Spine-Mets-CT-SEG, TCIA).
- [Spine CT and ultrasound, two ex-vivo phantoms](https://fidopt.io/dataset/SpineUSCT/): CT and acquired 3D ultrasound of a canine or lamb vertebra phantom, each in its own frame, with the authors' corresponding landmarks, for a rigid CT to ultrasound registration from the provider's pose.
- [Sunnybrook Cardiac Data](https://fidopt.io/dataset/Sunnybrook/): Cine MR of the heart, a short-axis stack of one patient at end diastole (fixed) and end systole (moving) (Sunnybrook Cardiac Data, the MICCAI 2009 left ventricle segmentation challenge).
- [Sunnybrook cine MR, left ventricle](https://fidopt.io/dataset/Sunnybrook_Seg/): Short-axis cine MR stack of the heart of one patient, at end diastole or end systole, with the left ventricular cavity drawn by a cardiologist (MICCAI 2009).
- [SynthRAD2025 CBCT/CT, thorax and abdomen](https://fidopt.io/dataset/SynthRAD2025_CBCTCT/): CT (fixed) and CBCT (moving) of the thorax or abdomen of one patient (SynthRAD2025, Task 2).
- [SynthRAD2025, CBCT to CT, thorax and abdomen](https://fidopt.io/dataset/SynthRAD2025_CBCTCT_Syn/): Cone-beam CT of one patient's thorax or abdomen and the CT to synthesise from it, the CT brought onto the CBCT's grid by the challenge (SynthRAD2025, Task 2).
- [SynthRAD2025 CBCT/CT, head and neck](https://fidopt.io/dataset/SynthRAD2025_HN_CBCTCT/): CT (fixed) and CBCT (moving) of the head and neck of one patient (SynthRAD2025, Task 2).
- [SynthRAD2025, CBCT to CT, head and neck](https://fidopt.io/dataset/SynthRAD2025_HN_CBCTCT_Syn/): Cone-beam CT of one head and neck patient and the CT to synthesise from it, which the challenge registered onto the CBCT's grid (SynthRAD2025, Task 2).
- [SynthRAD2025 MR/CT, head and neck](https://fidopt.io/dataset/SynthRAD2025_HN_MRCT/): CT (fixed) and MR (moving) of the head and neck of one patient (SynthRAD2025, Task 1).
- [SynthRAD2025, MR to CT, head and neck](https://fidopt.io/dataset/SynthRAD2025_HN_MRCT_Syn/): Head and neck MR of one patient and the CT to synthesise from it, the CT brought onto the MR's grid by the challenge (SynthRAD2025, Task 1).
- [SynthRAD2025 MR/CT, thorax and abdomen](https://fidopt.io/dataset/SynthRAD2025_MRCT/): CT (fixed) and MR (moving) of the thorax or abdomen of one patient (SynthRAD2025, Task 1).
- [SynthRAD2025, MR to CT, thorax and abdomen](https://fidopt.io/dataset/SynthRAD2025_MRCT_Syn/): The MR of one patient's thorax or abdomen and the CT to synthesise from it, the CT brought onto the MR's grid by the challenge (SynthRAD2025, Task 1).
- [SynthRAD2023 CBCT/CT, brain](https://fidopt.io/dataset/SynthRAD_BrainCBCTCT/): The CT (fixed) and the CBCT (moving) of one patient's brain, rigidly aligned as SynthRAD2023 Task 2 delivers them, with TotalSegmentator labels on both.
- [SynthRAD2023, CBCT to CT, brain](https://fidopt.io/dataset/SynthRAD_BrainCBCTCT_Syn/): Cone-beam CT of one patient's brain and the CT to synthesise from it, which the challenge brought onto the CBCT's grid (SynthRAD2023, Task 2).
- [SynthRAD2023 MR/CT, brain](https://fidopt.io/dataset/SynthRAD_BrainMRCT/): CT (fixed) and MR (moving) of one patient's brain, rigidly aligned as the challenge delivers them (SynthRAD2023, Task 1).
- [SynthRAD2023, MR to CT, brain](https://fidopt.io/dataset/SynthRAD_BrainMRCT_Syn/): Brain MR of one patient and the CT to synthesise from it, the CT brought onto the MR's grid by the challenge (SynthRAD2023, Task 1).
- [SynthRAD2023 CBCT/CT, pelvis](https://fidopt.io/dataset/SynthRAD_CBCTCT/): CT (fixed) and CBCT (moving) of the pelvis of one patient (SynthRAD2023, Task 2).
- [SynthRAD2023, CBCT to CT, pelvis](https://fidopt.io/dataset/SynthRAD_CBCTCT_Syn/): Cone-beam CT of one patient's pelvis and the CT to synthesise from it, the CT brought onto the CBCT's grid by the challenge (SynthRAD2023, Task 2).
- [SynthRAD2023 MR/CT, pelvis](https://fidopt.io/dataset/SynthRAD_MRCT/): CT (fixed) and MR (moving) of one patient's pelvis, rigidly aligned by the challenge (SynthRAD2023, Task 1).
- [SynthRAD2023, MR to CT, pelvis](https://fidopt.io/dataset/SynthRAD_MRCT_Syn/): Pelvic MR of one patient and the CT to synthesise from it, the CT brought onto the MR's grid by the challenge (SynthRAD2023, Task 1).
- [SynthStrip](https://fidopt.io/dataset/SynthStripMR/): One whole-head MR of a subject, adult, glioblastoma patient or infant, in one of nine contrasts and resolutions, with its brain mask (SynthStrip dataset, v1.5).
- [Synthetic cardiac cine MRI, healthy model motion](https://fidopt.io/dataset/SyntheticCineMR/): Two frames of a healthy cine MRI simulation generated from one STACOM 2011 volunteer, with the corresponding model mesh vertices.
- [TOM500 orbital MRI](https://fidopt.io/dataset/TOM500Orbit/): Coronal T2-weighted MRI of the orbits of a patient with thyroid eye disease at the first visit, with nine structures of both orbits outlined by hand (TOM500, Shanghai Ninth People's Hospital).
- [TartanAir](https://fidopt.io/dataset/TartanAir/): Two consecutive colour frames of a camera flying through a rendered world, indoor or outdoor: frames k (fixed) and k + 1 (moving) at the middle of the first Hard trajectory of a TartanAir environment.
- [Thyroid lobes, 3D ultrasound](https://fidopt.io/dataset/ThyroidLobeUS/): A 3D ultrasound volume of one thyroid lobe of a healthy volunteer, compounded from a tracked freehand sweep, with the lobe outlined by a medical expert with livewire (OpenCAS thyroid dataset, Wunderling et al. 2017, Magdeburg).
- [Tongue musculature MRI](https://fidopt.io/dataset/TongueMR/): 3D MR of the mouth of two healthy adults of one study, T2-weighted (BeLong, EATT4MND) or T1-weighted (BMC), with labels of the tongue muscles (Ribeiro et al. 2025), paired by us.
- [Tongue musculature MRI, four muscles](https://fidopt.io/dataset/TongueMR_Seg/): MR of the tongue of one adult with four muscle labels checked and corrected by hand.
- [STS-3D-Tooth](https://fidopt.io/dataset/ToothCBCT/): Dental cone-beam CT crops of two patients, the same side or region of the jaws in both, with the teeth labelled by hand (the 22 labelled crops of STS-3D-Tooth), paired by us.
- [TopBrain 2025/2026](https://fidopt.io/dataset/TopBrain/): Time-of-flight MR angiography (fixed) and CT angiography (moving) of the head of one stroke-centre patient, the arteries of the whole brain labelled on both (TopBrain training set, its 2025 labels).
- [TopBrain, brain arteries on MR angiography](https://fidopt.io/dataset/TopBrain_SegMRA/): Time-of-flight MR angiography of the head of one patient, with the arteries of the whole brain labelled (TopBrain, the 2025 labels).
- [TopCoW 2024](https://fidopt.io/dataset/TopCoW/): Time-of-flight MR angiography (fixed) and CT angiography (moving) of the head of one patient of a stroke centre, with the arteries of the circle of Willis labelled on both (TopCoW 2024 training set).
- [TopCoW 2024, MR angiography to CT angiography](https://fidopt.io/dataset/TopCoW_MRCT_Syn/): Time-of-flight MR angiography of the head of one stroke-centre patient (source) and the same patient's CT angiography (target), registered onto it by the corpus (TopCoW 2024 training set, University Hospital Zurich).
- [TopCoW, circle of Willis on MR angiography](https://fidopt.io/dataset/TopCoW_SegMRA/): A time-of-flight MR angiography of one patient's head, with the arteries of the circle of Willis labelled (TopCoW 2024).
- [TotalSegmentator CT](https://fidopt.io/dataset/TotalSegCT/): Routine clinical CT of any region of the body from the University Hospital Basel, with the 117 structures of TotalSegmentator's task total labelled (TotalSegmentator dataset 2.0.1).
- [TotalSegmentator MRI, any region](https://fidopt.io/dataset/TotalSegMR/): A routine clinical MR of any region, sequence and scanner, adult or child, from the University Hospital Basel or the Imaging Data Commons, the 50 structures of TotalSegmentator's task total_mr labelled (TotalSegmentator MRI dataset 3.0.0).
- [TotalSegmentator MRI](https://fidopt.io/dataset/TotalSegMRI/): Axial T1-weighted gradient-echo MR of the upper abdomen of two adults, one kind of image on both (fat, fat-suppressed, in or opposed phase), paired by us (TotalSegmentator MRI 3.0.0, University Hospital Basel).
- [TotalSegmentator MRI, 50 structures](https://fidopt.io/dataset/TotalSegMRI_Seg/): Axial T1-weighted gradient-echo MR of one adult's upper abdomen (fat, fat-suppressed, in phase or opposed phase), with the TotalSegmentator MRI dataset's masks of the structures it holds (University Hospital Basel).
- [TrackRAD2025, two frames of a sagittal cine MR sequence](https://fidopt.io/dataset/TrackRAD2025/): Two frames of one patient's sagittal cine MR on an MR-linac, the tracking target drawn by people on each: the first labelled frame and the one where the target lies farthest from it (TrackRAD2025).
- [TrackRAD2025, the tracking target on a cine MR frame](https://fidopt.io/dataset/TrackRAD2025_Seg/): One sagittal cine MR frame of a patient, with the tracking target drawn by people: the moving frame of a TrackRAD2025 registration pair.
- [UCSD-BMETS-Longitudinal](https://fidopt.io/dataset/UCSDBrainMets/): Contrast-enhanced T1 brain MR of one patient with brain metastases at the dataset's first two dates, weeks to years apart, skull-stripped and registered affinely to the first by the provider (UCSD-BMETS-Longitudinal).
- [UCSD-BMETS-Longitudinal, brain metastases](https://fidopt.io/dataset/UCSDBrainMets_Seg/): Contrast-enhanced T1 MR of the brain of one patient with brain metastases, skull-stripped by the provider, with the lesions segmented in the BraTS compartments (UCSD-BMETS-Longitudinal, TCIA).
- [UCSD-PTGBM, glioblastoma after treatment](https://fidopt.io/dataset/UCSDGliomaPostMR/): Brain MR of a patient treated for a high-grade glioma at UC San Diego, four sequences as one image on a 1 mm MNI grid, the four compartments of BraTS 2024 labelled (UCSD-PTGBM, TCIA).
- [ULS23, lesions in CT volumes of interest](https://fidopt.io/dataset/ULS23Lesions/): A CT volume of interest of 256 x 256 x 128 voxels centred on one lesion of the chest, abdomen or bones, the lesion segmented in 3D (ULS23 challenge, novel training data: DeepLesion and Radboudumc bone lesions).
- [UT-EndoMRI, uterus and ovaries on T2 fat-sat MRI](https://fidopt.io/dataset/UTEndoMRI/): Pelvic T2-weighted fat-suppressed MRI of one subject from the Texas Children’s Hospital Pavilion for Women subset of UT-EndoMRI, with the uterus and the ovaries contoured by hand.
- [UVDoc, measured paper geometry with rendered document texture](https://fidopt.io/dataset/UVDoc/): A flat document texture and its rendering on a measured, deformed sheet of paper, with the source UV map as known correspondence (UVDoc).
- [UltraCortex](https://fidopt.io/dataset/UltraCortex/): Brain T1 MR at 9.4 T of two healthy adults, skull-stripped, 0.6 to 0.8 mm, with a manual segmentation of the cortex and white matter of each hemisphere (UltraCortex).
- [UltraCortex, cortex and white matter at 9.4 T](https://fidopt.io/dataset/UltraCortex_Seg/): 9.4 T T1 MR of the brain of one adult with the cerebral cortex and white matter of each hemisphere segmented by hand.
- [Uterine Myoma MRI](https://fidopt.io/dataset/UterineMyomaMR/): Sagittal T2-weighted MRI of the pelvis of a woman with uterine myomas, with the uterine wall, cavity, myomas and nabothian cysts outlined by hand (UMD, Beijing Shijitan Hospital, Pan et al. 2024).
- [CT-vs-PET-Ventilation-Imaging, attenuation CT to Galligas ventilation PET](https://fidopt.io/dataset/VentilationCTPET_Syn/): The low-dose attenuation CT of one free-breathing session of a patient with lung cancer, resampled onto the PET grid, and as target the Galligas ventilation PET divided by its own 99th percentile inside the body.
- [VerSe](https://fidopt.io/dataset/VerSe/): Spine CT of two patients, from the cervical spine alone to the whole spine depending on the scan, paired by us from VerSe 2019 and 2020, with each vertebra labelled on both.
- [VerSe, vertebrae](https://fidopt.io/dataset/VerSe_Seg/): Spine CT of one patient, from the cervical spine alone to the whole spine, with one mask a vertebra (VerSe 2019 and 2020).
- [Vestibular-Schwannoma-SEG](https://fidopt.io/dataset/VestibularSchwannoma/): High-resolution T2 (fixed) and contrast-enhanced T1 (moving) MR of the head of one patient with a vestibular schwannoma, from one Gamma Knife session in a stereotactic frame, the T1 deformed by a known warp (Vestibular-Schwannoma-SEG).
- [Vestibular-Schwannoma-MC-RC](https://fidopt.io/dataset/VestibularSchwannomaMCRC/): T2-weighted head MR of a patient with a vestibular schwannoma, from routine follow-up at ten UK sites, the tumour outlined by a specialised company and reviewed by radiologists (Vestibular-Schwannoma-MC-RC, TCIA).
- [Vestibular-Schwannoma-MC-RC2](https://fidopt.io/dataset/VestibularSchwannomaMCRC2/): Contrast-enhanced T1 MR from the routine follow-up of a patient with a vestibular schwannoma referred to King's College Hospital, London, the tumour outlined by a network and accepted or corrected by experts (Vestibular-Schwannoma-MC-RC2, TCIA).
- [UCSD-VS-Longitudinal, vestibular schwannoma](https://fidopt.io/dataset/VestibularSchwannomaUCSD_Seg/): Contrast-enhanced T1 MR of the internal auditory canals at a vestibular schwannoma patient's first examination, the tumour outlined by a network, corrected by hand and approved by a neuroradiologist (UCSD-VS-Longitudinal, TCIA).
- [Vestibular-Schwannoma-SEG, tumour and cochlea](https://fidopt.io/dataset/VestibularSchwannoma_Seg/): High-resolution T2 MR of the head of one patient with a vestibular schwannoma, with the tumour and the cochlea drawn by the treating neurosurgeon and physicist.
- [Vestibular-Schwannoma-SEG, contrast-enhanced T1 to T2](https://fidopt.io/dataset/VestibularSchwannoma_T1T2_Syn/): Contrast-enhanced T1 MR of the head of a patient with a vestibular schwannoma (source) and the high-resolution T2 of the same Gamma Knife session (target), the head fixed in a stereotactic frame (Vestibular-Schwannoma-SEG, TCIA).
- [WAW-TACE](https://fidopt.io/dataset/WAWTACE/): One CT phase of a patient with hepatocellular carcinoma before a first transarterial chemoembolisation: the phase on which all their liver tumours were segmented (WAW-TACE, Medical University of Warsaw).
- [whole-spine T2 MR](https://fidopt.io/dataset/WholeSpineMR/): T2-weighted MR of the whole spine of one healthy volunteer, with each vertebra and disc from C1 to the sacrum, the spinal canal and the cord labelled by a network and corrected by hand (whole-spine, TotalSpineSeg's training data).
- [WxBS](https://fidopt.io/dataset/WxBS/): Two colour photographs of one outdoor scene from two viewpoints, most often at two times, by day and night or in two seasons: images 01 (fixed) and 02 (moving) of a WxBS pair (version 1.1).
- [York Cardiac MRI](https://fidopt.io/dataset/YorkCardiacMR/): Short-axis cardiac cine MR of a patient under 18 at end diastole (fixed) and end systole (moving), with the left ventricular cavity and myocardium drawn by hand on both (York University's cardiac MRI dataset).
- [York cardiac MRI, left ventricle](https://fidopt.io/dataset/YorkCardiacMR_Seg/): Short-axis cine MR stack of the heart of a patient under 18, at end diastole or end systole, the left ventricular cavity and the myocardium drawn by hand (York Cardiac MRI).
- [ZephIR worm (freely moving C. elegans, whole-brain imaging)](https://fidopt.io/dataset/ZephIRWorm/): Two volumes of one fluorescence recording of a freely moving C. elegans head, 16 to 123 seconds apart, with the 178 tracked neurons given a point in both, placed or checked by people (ZephIR).
- [µ-RegPro](https://fidopt.io/dataset/muRegPro/): Transrectal ultrasound (fixed) and T2 MR (moving) of the prostate of one patient (µ-RegPro challenge, MICCAI 2023, holdout test set).
- [µ-RegPro, prostate on transrectal ultrasound](https://fidopt.io/dataset/muRegPro_SegUS/): Transrectal ultrasound of the prostate of one patient, with the gland contoured or corrected by hand (µ-RegPro, MICCAI 2023).