fidopt Interactive view
CLEM-Reg cellular volumes

CLEM-Reg, Airyscan fluorescence to volume electron microscopy

One cell specimen imaged twice, an Airyscan fluorescence volume (moving) and a volume electron microscopy (fixed), with manually placed BigWarp correspondences.

2 test pairscellssame specimenfixed EM, moving FLUORESCENCEaligned once by the benchmarkresearch only
Look at the images
Read before comparing (5)
  • Images. The moving image is the CZI's MitoTracker channel, identified from its metadata. The fixed image is the author-aligned, cropped and downscaled EM TIFF that matches the released landmarks, not a composite holding warped fluorescence. Both keep their native intensities, voxels and grids.
  • Units. Calibration stays in micrometres, including non-rounded TIFF resolution and slice spacing. The landmarks are in ImageJ image coordinates starting at zero, as BigWarp uses them, not CZI tile offsets: S-BSST1075 starts at storage tile (12,12), recorded in provenance.
  • Alignment. Each pair gets one start from the intensities alone, an elastix translation (elastix-translation) on mutual information inside each image's body, written in the moving image's header and points. Every active landmark pair is scored.
  • Baseline. With no registration the points lie 0.56 µm apart on S-BSST707 (145 points) and 9.10 µm on S-BSST1075 (42 points), where the cell's fluorescence lies beside its EM outline. The difference in scale and shape between the two volumes is left to the methods.
  • Caveats. Only two cellular specimens, author-selected reference landmarks and mixed or unspecified source licences: keep results apart.

No method has a result on every pair of this dataset yet.

AccuracySmoothnessCost
#MethodTRE µmChangerTRESDlogJFolds %Time sRAM GBGPU GBImages
No registration4.83 ±54.270.0663 ±0.68970.0000.00

TRE: distance between matching landmarks. rTRE: the TRE over the length of the image's diagonal, to compare datasets of other sizes and units. SDlogJ: how irregular the deformation is, 0 is perfectly smooth. Folds: share of the image where the deformation folds over itself.

Pair by pair

TRE µm12
No registration0.569.10

Click a score to look at that result: the fixed image, and over it the moving image after registration, with the annotations. Underlined scores have their image; for the others you see the pair without the result. A green cell gained against no registration on that pair, a red one lost.

About the data

Test pairs
The two released specimens are the test cases. No independent development pair is available: a shared cell culture and donor do not make another pair independent. S-BSST1175/EMPIAR-11666 is excluded pending coordinate-frame clarification: its active moving landmarks reach y = 68.59 µm, outside the CZI's 63.50 µm height, and no axis swap, rotation, rescaling or point deletion is inferred to force agreement.
Truth
landmarks by experts 145 and 42 active source correspondences for S-BSST707 and S-BSST1075, all scored. Inactive source rows are excluded.
Licence
EMPIAR volumes are CC0; no explicit reusable image licence was identified for these two BioStudies light-microscopy records. Local evaluation does not establish redistribution permission.