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CREMI

MICCAI Challenge on
Circuit Reconstruction from Electron Microscopy Images

Leaderboard Neuron Segmentation

Results for the neuron segmentation category, averaged over all samples.

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Group Submission CREMI score VOI split VOI merge ARAND
JRC MTLR 0.269 0.395 0.130 0.138
PCH UNet_mis 0.272 0.453 0.113 0.131
PCH interp_a 0.274 0.472 0.113 0.129
PCH interp 0.275 0.473 0.114 0.129
JRC MALAMCv2 0.276 0.490 0.089 0.132
IAL CMaskMC2 0.276 0.348 0.152 0.157
PCH sff_aug 0.277 0.471 0.118 0.130
PCH UNet_inp 0.277 0.438 0.131 0.137
PCH sff_a 0.277 0.473 0.119 0.131
IAL CMaskSP4 0.280 0.371 0.159 0.149
PCH UNet_no 0.285 0.475 0.129 0.135
JRC MALA v2 0.286 0.479 0.127 0.135
VIDAR MALAv2 0.286 0.479 0.127 0.135
PCH UNet_aut 0.286 0.479 0.127 0.135
JRC MALALMC2 0.294 0.400 0.168 0.154
JRC MALAMCv3 0.300 0.584 0.062 0.140
IAL CMaskMC 0.305 0.341 0.175 0.184
PCH UNet_dip 0.310 0.501 0.158 0.146
PCH UNet_dim 0.312 0.513 0.180 0.141
IAL CMaskMWS 0.314 0.361 0.162 0.196
IAL spUNetMC 0.317 0.519 0.125 0.156
IAL CMaskSP1 0.317 0.360 0.186 0.187
JRC MALAMC 0.317 0.497 0.170 0.152
JRC MTLSD_L 0.318 0.386 0.153 0.190
IAL UnetLRLC 0.325 0.463 0.188 0.164

Legend

CREMI score
The geometric mean of (VOI split + VOI merge) and ARAND.
VOI split and merge
The Variation of Information between a segmentation X and ground truth Y. The split and merge parts correspond to the conditional entropies H(X|Y) and H(Y|X), respectively.
ARAND
The Adapted Rand Error, i.e., 1.0 - Rand F-Score.

For each value, lower is better.

Leaderboard Synaptic Cleft Detection

Results for the synaptic cleft detection category, averaged over all samples.

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Group Submission CREMI score FP FN 1 - F-score ADGT ADF
VCG FgUPlus 57.90 137412.7 4763.3 0.160 90.99 24.81
DIVE BouUNet 81.45 75985.0 21974.0 0.160 76.66 86.24
I2I CleftB1 64.97 80004.7 19895.0 0.158 90.98 38.97
DIVE cleft_hi 107.24 44844.3 52063.7 0.158 94.14 120.33
HSS HSZ 90.11 65092.3 25807.3 0.154 99.61 80.61
3DEM ABC_BC 62.21 99221.7 10981.0 0.151 75.79 48.63
I2I CleftB 74.31 65334.0 21669.0 0.142 92.36 56.26
VCG FgSm0805 54.23 111486.0 4917.0 0.142 84.04 24.43
I2I CSparSep 75.79 71650.0 18918.3 0.140 72.06 79.52
CMM UNet50 69.31 65762.0 12634.7 0.139 97.45 41.17
JRC DTU-1 72.21 85169.0 13607.3 0.131 106.31 38.11
DIVE WeitUNet 78.12 54372.7 24480.3 0.128 71.51 84.73
3DEM BC_BC 66.71 82113.3 13347.3 0.126 79.96 53.46
DLST DLST003 91.71 33118.7 35934.7 0.125 58.14 125.27
JRC DTU-2 67.56 70761.3 10069.3 0.123 109.67 25.46
DLST DLST002 75.46 56645.7 17498.3 0.119 65.93 85.00
timliu mynnUNet 75.11 49973.7 19071.3 0.117 64.50 85.71
DKFZ-MIC nnUNet 74.96 49914.0 18981.3 0.117 64.46 85.46
HSS 3DUNet04 79.33 29732.0 27514.3 0.113 53.22 105.44
DIVE ex19t5 315.97 64192.0 1757.3 0.112 600.79 31.15
VCG FgSm0808 57.34 75120.7 9109.7 0.107 72.74 41.94
DIVE exp19lst 90.80 25114.7 21554.0 0.107 117.39 64.21
DLST DLST001 71.19 53908.0 14839.0 0.106 69.02 73.36
HSS 3DUNet 65.34 43440.3 22443.3 0.106 63.26 67.43
VCG FgUPlus8 58.66 65345.7 11887.0 0.101 70.36 46.96

Legend

CREMI score
The mean of ADGT and ADF. We are not including the F-Score for now, as our current way of computing it can lead to unfair comparison. We are working on a more robust measure and will update the results accordingly.
FP, FN, and F-Score
The False Positives, False Negatives, and the resulting F-Score in the clefts detection volume. See metrics for details.
ADGT
The average distance of any found cleft voxel to the closest ground truth cleft voxel.
ADF
The average distance of any ground truth cleft voxel to the closest found cleft voxel.

For each value, lower is better (F-Score shown as 1 - F-Score).

Leaderboard Synaptic Partner Identification

Results for the synaptic partner identification category, averaged over all samples.

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Group Submission CREMI score FP FN
PNI asyn_mod 0.423 367.667 262.333
NO2 lr_balan 0.447 175.333 314.000
HCBS Tr66_80K 0.449 223.000 286.667
HCBS Tr66comb 0.451 219.000 292.333
DIVE PTR_V2 0.453 162.667 333.667
IAL PSP_unar 0.461 266.667 281.000
IAL PSP_full 0.464 187.333 310.000
HCBS PrnTrn66 0.465 178.667 322.333
PNI asyn_at0 0.468 293.333 297.000
HCBS Tr66t-01 0.469 182.667 318.667
PNI asyn_at1 0.490 274.333 314.667
PNI asyn_ori 0.493 310.000 302.333
NO2 lr_affin 0.567 118.333 450.000
AnonumoysGroup PrTrn66 0.620 238.000 451.667
  • 14 items

Legend

CREMI score
1 - F-Score of the FP and FN.
FP, FN
The False Positives and False Negatives synaptic partner pairs. See metrics for details.

For each value, lower is better.