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Cortical layers on histological sections (2D), one brain, segmentation

BigBrain cortical layers, manual annotations

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.

10 test casesbrain corteximage HISTOLOGY2D, distances in mmresearch only
Look at the images
Read before comparing (6)
  • Truth. Layers drawn by hand on 1 to 8 strips of cortex a section, from the pial surface to the white matter, on rescans of the sections at 5 µm, checked by three anatomists, then registered to these 20 µm sections; every pixel outside a strip, unlabelled cortex included, is taken out of both the truth and the prediction (ignore), so a method is scored on how it splits the strips into layers, not on where it puts cortex.
  • Ranked apart. One donor: twelve sections of one brain, 1.6 to 120 mm apart; strips of two sections lie within 2 mm of each other in the plane only for sections 9.9 mm apart or more. Section s4080 holds no layer IV.
  • Images. The section as delivered (raw_<k>.mnc), 20 µm a pixel, cut to the box of its strips grown by 2.56 mm; nothing is resampled. Some boxes hold blank tiles of the release. The smoother second rendering of each section (geo_<k>.mnc) is not given.
  • Tolerance. 0.1 mm, 5 pixels: at the default 1 mm, layers shifted by 0.2 mm keep a surface Dice of 1.00; at 0.1 mm they fall to 0.51 (s4080).
  • Start. Every strip pixel named one layer scores a mean Dice over the layers of 0.07 to 0.09 on the test sections; the best single layer, III on most, reaches 0.44 to 0.51 alone.
  • Licence. Non-commercial: research board only.

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

Case by case

Click a score to look at that result: the image, the truth in green and the method's map in red. Underlined scores have their image; for the others you see the case without the result.

About the data

Test cases
10 test sections drawn with seed 2026 among the 12 usable annotated ones, the other 2 for development; s1600 is held out, its strip lying on blank pixels of the image. All are sections of one brain: ten correlated cases of one donor, not ten subjects.
Truth
contours by experts the six cortical layers, I to VI, drawn by hand on a few strips of cortex of each section (Wagstyl et al. 2020, training data of the BigBrain layer atlas); the rest of the section is out of the scoring
Licence
CC BY-NC-SA 4.0 (the release's License.txt)
2 cases for tuning, never tested

s6316, s0301