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Serial EM, known in-plane deformation

ISBI 2012 EM sections, known in-plane deformation

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.

10 test pairsdrosophila ventral nerve cordsame sectionfixed ELECTRON MICROSCOPY, moving ELECTRON MICROSCOPY2D, distances in nmdelivered alignedresearch only
Look at the images
Read before comparing (5)
  • Truth. Both sides are the same original section before the warp, since a known warp applied to a neighbouring section would not make its correspondence exact. The points lie at least 20 pixels (80 nm) inside every border, beyond the 16-pixel (64 nm) bound on each deformation component.
  • Units. The TIFF headers give 4 nm a pixel, so coordinates and distances are in nanometres; the build fields amplitude_mm and spacing_mm hold nanometres here (16 and 64 pixels, SNEMI3D's warp in pixels).
  • Labels. The provider's membrane maps, test labels included since 2016, are not read: the ISBI 2012 segmentation task on these sections is not built, since it would hold the same images twice.
  • Start. With no registration the mean landmark error of a test section is 19.0 to 24.5 nm (4.8 to 6.1 pixels), median 22.1 nm. Fixed and moving are one image before the warp, so the line checks a method's convention and interpolation more than it separates methods.
  • Licence. The page states no licence and the challenge rules once limited training to the training stack: ask before any use beyond research.

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

Pair by pair

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
10 test sections drawn with seed 2026 from the provider's 30-section test stack and 10 development sections from its 30-section training stack. Both stacks come from one larva and neighbouring sections are correlated: a stack-separated synthetic track, not an animal-independent split.
Truth
landmarks a known deformation One hundred interior image points paired through the inverse of the corpus-added B-spline deformation of that same section.
Licence
none stated: the challenge page offers the training and test stacks for download and names no terms
10 pairs for tuning, never tested

train_z008, train_z028, train_z006, train_z025, train_z022, train_z024, train_z020, train_z011, train_z015, train_z000