IWC multi-step task

Task 9: Multiplex tissue imaging and cell neighborhoods

What the task asks for

Correct, stitch and register ten imaging cycles, segment nuclei in four tissue cores, assign cell phenotypes and test which phenotypes sit next to each other.

9 scored results9 required18 runs scored

Codex GPT-5.6 Luna

6 of 6 runs scored
Galaxy-API code 0.704 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.740
All results pass1 of 3 runsruns in which every scored result passes
run 11.0009/9run 20.5565/9run 30.5565/9
Open-ended code 0.000 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.000
All results pass0 of 3 runsruns in which every scored result passes
run 10.0000/9run 20.0000/9run 30.0000/9

Codex GPT-5.6 Sol

6 of 6 runs scored
Galaxy-API code 1.000 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 1.000
All results pass3 of 3 runsruns in which every scored result passes
run 11.0009/9run 21.0009/9run 31.0009/9
Open-ended code 0.259 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.625
All results pass0 of 3 runsruns in which every scored result passes
run 10.0000/9run 20.3333/9run 30.4444/9

DeepSeek V4 Pro via Codex

6 of 6 runs scored
Galaxy-API code 0.889 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.936
All results pass2 of 3 runsruns in which every scored result passes
run 11.0009/9run 21.0009/9run 30.6676/9
Open-ended code 0.000 BixBench3 acc (share of results that pass), averaged over 3 of 3 runs continuous score 0.002
All results pass0 of 3 runsruns in which every scored result passes
run 10.0000/9run 20.0000/9run 30.0000/9

Three measures. Every required result gets a score from 0 to 1 by comparison with the reference. Passing requires a score of at least 0.80 and compliance with the required content, method and output instructions. BixBench3 acc is the share of results that pass. The continuous score is the plain average of all the result scores, with no pass mark. For example, run 2 of GPT-5.6 Luna with Galaxy-API code scored 1.000, 1.000, 1.000, 1.000, 1.000, 0.276, 0.000, 0.000 and 0.000 on its 9 results. 5 of them pass, so BixBench3 acc = 5/9 = 0.556; the average of all 9 scores is 0.586, the continuous score. A third measure, all results pass, counts a run only when every scored result passes, which is the share of runs that delivered the whole analysis correctly. A failing result still contributes its numerical score to the continuous average. A score above 0.80 does not excuse an incorrect method, missing member or an explicitly required output format. Each card averages the scored runs of this task.

Error analysis

BixBench3 acc, Galaxy-API code vs Open-ended code: GPT-5.6 Luna 0.704 vs 0.000; GPT-5.6 Sol 1.000 vs 0.259; DeepSeek V4 Pro 0.889 vs 0.000.

What Galaxy added

Galaxy has the whole imaging toolchain the task describes, from illumination correction, stitching and core detection to deep-learning nuclear segmentation, phenotyping and spatial statistics. Galaxy runs reproduced the reference image geometry exactly and passed the first four results in all nine runs. Open-ended runs substituted other methods for parts of the chain, in some cases because a package could not be installed on the container, and their mosaics, core crops or nuclei differed, so nearly every later result failed.

Why Galaxy did not do better

Three Galaxy runs lost later results through the agents' own choices. Two ran phenotyping without the log transform, and one of these also delivered two cores swapped; the third built the spatial graph on a reduced-dimension embedding instead of cell positions. One version of the neighborhood tool failed with a shared-storage error, and the runs recovered with another version.

Run-level details (4)
  • Open-ended code runs with GPT-5.6 Luna and DeepSeek V4 Pro used other illumination correction, stitching, core detection or nuclear segmentation, so their mosaics, core crops and masks differed from the reference. GPT-5.6 Sol stitched like the reference, but its core crops were about 60 pixels smaller, and it segmented nuclei with its own watershed because the deep-learning segmentation package could not be installed on the container.
  • The second Open-ended run with DeepSeek V4 Pro wrote its illumination profiles without the required file suffix, so all 20 files counted as missing.
  • The third Galaxy run with DeepSeek V4 Pro and the second with GPT-5.6 Luna ran phenotyping without the log transform. Their phenotype labels agreed poorly with the reference (F1 0.41), and the interaction and enrichment results failed with them. The second GPT-5.6 Luna run also delivered cores 3 and 4 swapped for results 7 to 9.
  • The third Galaxy run with GPT-5.6 Luna built the spatial graph on a PCA embedding instead of cell positions, after naming a coordinate key that does not exist.
Instruction, format and method errors (2)

Every run

The task asks the agent to return a numbered list of results, each a file or a folder of files. The columns on the right give the score of each required result in each run, from 0 to 1 against the reference, under the result's number and name; the task text and the scoring table below describe each one. Green marks a passing result. Failing cells link to the reasons below, including instruction and format errors even when the numerical score is at least 0.80. In each row, BixBench3 acc is the number of green cells divided by the number of results, and the continuous score is the average of all the result scores in the row. Tokens are input (including cached input) plus output tokens; minutes are the wall time of the run. Under Records, Trace opens the run's task text, agent event log, final message and returned files in the lab's run trace dataset on Hugging Face, and History opens the usegalaxy.org history that a Galaxy-API code run worked in.

Score of each required result
ModelConditionRunBixBench3 acc
share passing		Continuous score TokensMinutesRecords1illumination2registered images3core images4nuclear masks5cell measurements6phenotypes7spatial graphs8interactions9neighborhood enrichment
GPT-5.6 LunaGalaxy-API code1trial run9/9 = 1.0001.0008.8M663Trace
History		1.00 Passed1.00 Passed1.00 Passed0.99 Passed0.99 Passed0.99 Passed0.99 Passed1.00 Passed1.00 Passed
25/9 = 0.5560.58629.0M852Trace
History		1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed0.27Member0.00Member0.00Member0.00Member
35/9 = 0.5560.63550.3M1260Trace
History		1.00 Passed1.00 Passed1.00 Passed1.00 Passed0.00Format1.00 Passed0.00Member0.67Member0.03Member
Open-ended code1trial run0/9 = 0.0000.00012.0M38Trace0.00Content0.00Content0.00Member0.00Member0.00Member0.00Member0.00Member0.00Member0.00Member
20/9 = 0.0000.0003.5M11Trace0.00Content0.00Content0.00Member0.00Member0.00Member0.00Member0.00Member0.00Member0.00Member
30/9 = 0.0000.0003.0M10Trace0.00Content0.00Content0.00Member0.00Member0.00Member0.00Member0.00Member0.00Member0.00Member
GPT-5.6 SolGalaxy-API code19/9 = 1.0001.0009.1M641Trace
History		1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed
29/9 = 1.0001.00014.8M599Trace
History		1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed
39/9 = 1.0001.0005.2M623Trace
History		1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed
Open-ended code10/9 = 0.0000.48715.4M30Trace0.02Content0.72Content0.00Member0.80Member0.14Member0.49Member0.77Member0.69Member0.72Member
23/9 = 0.3330.64712.3M23Trace0.62Content0.95 Passed0.00Member0.80Member0.00Member0.75Member0.77Member0.95 Passed0.95 Passed
34/9 = 0.4440.74114.0M19Trace0.95 Passed0.99 Passed0.00Member0.79Member0.70Member0.62Member0.73Member0.92 Passed0.93 Passed
DeepSeek V4 ProGalaxy-API code19/9 = 1.0001.00018.5M394Trace
History		1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed
29/9 = 1.0001.0007.1M608Trace
History		1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed1.00 Passed
36/9 = 0.6670.80718.4M358Trace
History		1.00 Passed1.00 Passed1.00 Passed0.99 Passed0.99 Passed0.27Member0.99 Passed0.45Member0.53Member
Open-ended code10/9 = 0.0000.0076.8M26Trace0.05Content0.00Content0.00Member0.00Member0.00Member0.00Member0.00Member0.00Member0.00Member
20/9 = 0.0000.00019.7M37Trace0.00Instruction0.00Content0.00Member0.00Member0.00Member0.00Member0.00Member0.00Member0.00Member
30/9 = 0.0000.0008.6M16Trace0.00Content0.00Content0.00Member0.00Member0.00Member0.00Member0.00Member0.00Member0.00Member

Why results did not pass

  1. GPT-5.6 Luna / Galaxy-API code / run 2 → result 6 (phenotypes)
    • Content: Content score below 0.80. Value: 0.276984. Required minimum: 0.8.
      • Category agreement (F1): 0.40673 to 0.744003 (4 checks)
      • Numerical agreement (CCC): 0.364874 to 0.599745 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.243934
      • member 2: 0.445806
      • member 3: 0.236346
      • member 4: 0.181851
  2. GPT-5.6 Luna / Galaxy-API code / run 2 → result 7 (spatial graphs)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0.0329008 to 0.852826 (3 checks)
      • Numerical agreement (CCC): 0.419377 to 0.589485 (2 checks)
      • Present, finite data cells (F1): 0.0329008 to 0.852826 (2 checks)
      • Required content missing or unreadable: 0 (3 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0.000165986
  3. GPT-5.6 Luna / Galaxy-API code / run 2 → result 8 (interactions)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0.852826
      • Numerical agreement (CCC): 0.161442 to 0.828215 (3 checks)
      • Required content missing or unreadable: 0 (2 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.161442
      • member 2: 0
      • member 3: 0.225987
  4. GPT-5.6 Luna / Galaxy-API code / run 2 → result 9 (neighborhood enrichment)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0.852826
      • Numerical agreement (CCC): 0.240166 to 0.851853 (3 checks)
      • Required content missing or unreadable: 0 (2 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.341855
      • member 2: 0
      • member 3: 0.20482
    • Check: A required check is below its minimum. Required minimum: 0.9.
      • Numerical agreement (CCC): 0.240166 to 0.851853 (3 checks)
  5. GPT-5.6 Luna / Galaxy-API code / run 3 → result 5 (cell measurements)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (8 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
    • Format: Named stored field is missing: raw/XTask requirement: 5. final_answer/05_cell_measurements/{core}.csv CSV + H5AD The measurement CSV and a same-core .h5ad with log1p marker matrix X, raw intensities in raw/X and their identities in raw/var. CSV/H5AD preserve CellID, X_centroid, Y_centroid and every measured marker. Files: {core}.csv, {core}.h5ad.
    • Format: Named stored field is missing: raw/varTask requirement: 5. final_answer/05_cell_measurements/{core}.csv CSV + H5AD The measurement CSV and a same-core .h5ad with log1p marker matrix X, raw intensities in raw/X and their identities in raw/var. CSV/H5AD preserve CellID, X_centroid, Y_centroid and every measured marker. Files: {core}.csv, {core}.h5ad.
    • Format: Named stored field is missing: raw/XTask requirement: 5. final_answer/05_cell_measurements/{core}.csv CSV + H5AD The measurement CSV and a same-core .h5ad with log1p marker matrix X, raw intensities in raw/X and their identities in raw/var. CSV/H5AD preserve CellID, X_centroid, Y_centroid and every measured marker. Files: {core}.csv, {core}.h5ad.
    • Format: Named stored field is missing: raw/varTask requirement: 5. final_answer/05_cell_measurements/{core}.csv CSV + H5AD The measurement CSV and a same-core .h5ad with log1p marker matrix X, raw intensities in raw/X and their identities in raw/var. CSV/H5AD preserve CellID, X_centroid, Y_centroid and every measured marker. Files: {core}.csv, {core}.h5ad.
    • Format: Named stored field is missing: raw/XTask requirement: 5. final_answer/05_cell_measurements/{core}.csv CSV + H5AD The measurement CSV and a same-core .h5ad with log1p marker matrix X, raw intensities in raw/X and their identities in raw/var. CSV/H5AD preserve CellID, X_centroid, Y_centroid and every measured marker. Files: {core}.csv, {core}.h5ad.
    • Format: Named stored field is missing: raw/varTask requirement: 5. final_answer/05_cell_measurements/{core}.csv CSV + H5AD The measurement CSV and a same-core .h5ad with log1p marker matrix X, raw intensities in raw/X and their identities in raw/var. CSV/H5AD preserve CellID, X_centroid, Y_centroid and every measured marker. Files: {core}.csv, {core}.h5ad.
    • Format: Named stored field is missing: raw/XTask requirement: 5. final_answer/05_cell_measurements/{core}.csv CSV + H5AD The measurement CSV and a same-core .h5ad with log1p marker matrix X, raw intensities in raw/X and their identities in raw/var. CSV/H5AD preserve CellID, X_centroid, Y_centroid and every measured marker. Files: {core}.csv, {core}.h5ad.
    • Format: Named stored field is missing: raw/varTask requirement: 5. final_answer/05_cell_measurements/{core}.csv CSV + H5AD The measurement CSV and a same-core .h5ad with log1p marker matrix X, raw intensities in raw/X and their identities in raw/var. CSV/H5AD preserve CellID, X_centroid, Y_centroid and every measured marker. Files: {core}.csv, {core}.h5ad.
  6. GPT-5.6 Luna / Galaxy-API code / run 3 → result 7 (spatial graphs)
    • Content: Content score below 0.80. Value: 1.3537e-08. Required minimum: 0.8.
      • Matching records (F1): 6.08099e-05 to 0.000285833 (4 checks)
      • Numerical agreement (CCC): 0.5 to 0.568816 (4 checks)
      • Present, finite data cells (F1): 6.08099e-05 to 0.000285833 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 4.5122e-08
      • member 2: 4.22593e-09
      • member 3: 1.84892e-09
      • member 4: 2.9511e-09
  7. GPT-5.6 Luna / Galaxy-API code / run 3 → result 8 (interactions)
    • Content: Content score below 0.80. Value: 0.678406. Required minimum: 0.8.
      • Numerical agreement (CCC): 0.640763 to 0.73715 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.641401
      • member 2: 0.694309
      • member 3: 0.640763
      • member 4: 0.73715
  8. GPT-5.6 Luna / Galaxy-API code / run 3 → result 9 (neighborhood enrichment)
    • Content: Content score below 0.80. Value: 0.0337544. Required minimum: 0.8.
      • Numerical agreement (CCC): 0.0160759 to 0.0460013 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.0160759
      • member 2: 0.0302003
      • member 3: 0.0427403
      • member 4: 0.0460013
    • Check: A required check is below its minimum. Required minimum: 0.9.
      • Numerical agreement (CCC): 0.0160759 to 0.0460013 (4 checks)
  9. GPT-5.6 Luna / Open-ended code / run 1 → result 1 (illumination)
    • Content: Content score below 0.80. Value: 2.44498e-05. Required minimum: 0.8.
      • Required fields: 0.00022935 to 0.11047 (20 checks)
  10. GPT-5.6 Luna / Open-ended code / run 1 → result 2 (registered images)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Image agreement: 0
      • Numerical agreement (CCC): 0
  11. GPT-5.6 Luna / Open-ended code / run 1 → result 3 (core images)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Image agreement: 0 to 0.409703 (12 checks)
      • Numerical agreement (CCC): 0 (4 checks)
      • Required content missing or unreadable: 0 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  12. GPT-5.6 Luna / Open-ended code / run 1 → result 4 (nuclear masks)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Image agreement: 0 (8 checks)
      • Required content missing or unreadable: 0 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  13. GPT-5.6 Luna / Open-ended code / run 1 → result 5 (cell measurements)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0 (8 checks)
      • Numerical agreement (CCC): 0 (8 checks)
      • Present, finite data cells (F1): 0 (8 checks)
      • Required content missing or unreadable: 0 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  14. GPT-5.6 Luna / Open-ended code / run 1 → result 6 (phenotypes)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Category agreement (F1): 0 (4 checks)
      • Matching records (F1): 0 (12 checks)
      • Numerical agreement (CCC): 0 (4 checks)
      • Present, finite data cells (F1): 0 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  15. GPT-5.6 Luna / Open-ended code / run 1 → result 7 (spatial graphs)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0 (12 checks)
      • Numerical agreement (CCC): 0 (8 checks)
      • Present, finite data cells (F1): 0 (8 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  16. GPT-5.6 Luna / Open-ended code / run 1 → result 8 (interactions)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (8 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  17. GPT-5.6 Luna / Open-ended code / run 1 → result 9 (neighborhood enrichment)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Category agreement (F1): 0.606796 to 0.688462 (4 checks)
      • Matching records (F1): 0 (4 checks)
      • Numerical agreement (CCC): 0.0456963 to 0.198115 (4 checks)
      • Present, finite data cells (F1): 0.777358 to 0.890411 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
    • Check: A required check is below its minimum. Required minimum: 0.9.
      • Numerical agreement (CCC): 0.0456963 to 0.198115 (4 checks)
  18. GPT-5.6 Luna / Open-ended code / run 2 → result 1 (illumination)
    • Content: Content score below 0.80. Value: 2.73327e-05. Required minimum: 0.8.
      • Required fields: 0.000200769 to 0.136063 (20 checks)
  19. GPT-5.6 Luna / Open-ended code / run 2 → result 2 (registered images)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Image agreement: 0
      • Numerical agreement (CCC): 0
  20. GPT-5.6 Luna / Open-ended code / run 2 → result 3 (core images)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Image agreement: 0 to 0.937545 (12 checks)
      • Numerical agreement (CCC): 0 (4 checks)
      • Required content missing or unreadable: 0 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  21. GPT-5.6 Luna / Open-ended code / run 2 → result 4 (nuclear masks)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Image agreement: 0 to 0.233888 (8 checks)
      • Required content missing or unreadable: 0 (3 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0.000258528
  22. GPT-5.6 Luna / Open-ended code / run 2 → result 5 (cell measurements)
    • Content: Content score below 0.80. Value: 1.54212e-20. Required minimum: 0.8.
      • Matching records (F1): 0 to 0.00187315 (12 checks)
      • Numerical agreement (CCC): 0 to 0.132465 (12 checks)
      • Present, finite data cells (F1): 0 to 0.00187315 (12 checks)
      • Required fields: 0.923077 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 6.16848e-20
  23. GPT-5.6 Luna / Open-ended code / run 2 → result 6 (phenotypes)
    • Content: Content score below 0.80. Value: 2.29227e-14. Required minimum: 0.8.
      • Category agreement (F1): 0 to 0.0779221 (4 checks)
      • Matching records (F1): 0 to 0.00187315 (12 checks)
      • Numerical agreement (CCC): 0 to 0.0955825 (4 checks)
      • Present, finite data cells (F1): 0 to 0.00187315 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 9.16908e-14
  24. GPT-5.6 Luna / Open-ended code / run 2 → result 7 (spatial graphs)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (12 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  25. GPT-5.6 Luna / Open-ended code / run 2 → result 8 (interactions)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (8 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  26. GPT-5.6 Luna / Open-ended code / run 2 → result 9 (neighborhood enrichment)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (8 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  27. GPT-5.6 Luna / Open-ended code / run 3 → result 1 (illumination)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (20 checks)
      • Required fields: 0 (40 checks)
  28. GPT-5.6 Luna / Open-ended code / run 3 → result 2 (registered images)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Image agreement: 0
      • Numerical agreement (CCC): 0
  29. GPT-5.6 Luna / Open-ended code / run 3 → result 3 (core images)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Image agreement: 0 to 0.911582 (12 checks)
      • Numerical agreement (CCC): 0 (4 checks)
      • Required content missing or unreadable: 0 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  30. GPT-5.6 Luna / Open-ended code / run 3 → result 4 (nuclear masks)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Image agreement: 0 (8 checks)
      • Required content missing or unreadable: 0 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  31. GPT-5.6 Luna / Open-ended code / run 3 → result 5 (cell measurements)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (12 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  32. GPT-5.6 Luna / Open-ended code / run 3 → result 6 (phenotypes)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (12 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  33. GPT-5.6 Luna / Open-ended code / run 3 → result 7 (spatial graphs)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (12 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  34. GPT-5.6 Luna / Open-ended code / run 3 → result 8 (interactions)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (8 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  35. GPT-5.6 Luna / Open-ended code / run 3 → result 9 (neighborhood enrichment)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (8 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  36. GPT-5.6 Sol / Open-ended code / run 1 → result 1 (illumination)
    • Content: Content score below 0.80. Value: 0.020928. Required minimum: 0.8.
      • Required fields: 0.0178467 to 0.999985 (25 checks)
  37. GPT-5.6 Sol / Open-ended code / run 1 → result 2 (registered images)
    • Content: Content score below 0.80. Value: 0.722362. Required minimum: 0.8.
      • Image agreement: 0.998113
      • Numerical agreement (CCC): 0.723727
  38. GPT-5.6 Sol / Open-ended code / run 1 → result 3 (core images)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Image agreement: 0 to 0.985697 (12 checks)
      • Numerical agreement (CCC): 0 (4 checks)
      • Required content missing or unreadable: 0 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  39. GPT-5.6 Sol / Open-ended code / run 1 → result 4 (nuclear masks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.764874
      • member 2: 0.790473
  40. GPT-5.6 Sol / Open-ended code / run 1 → result 5 (cell measurements)
    • Content: Content score below 0.80. Value: 0.148132. Required minimum: 0.8.
      • Matching records (F1): 0.952125 to 0.984765 (12 checks)
      • Numerical agreement (CCC): 0.466646 to 0.69602 (12 checks)
      • Present, finite data cells (F1): 0.942321 to 0.984765 (12 checks)
      • Required fields: 0.989691 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.128734
      • member 2: 0.198491
      • member 3: 0.130645
      • member 4: 0.134657
  41. GPT-5.6 Sol / Open-ended code / run 1 → result 6 (phenotypes)
    • Content: Content score below 0.80. Value: 0.496399. Required minimum: 0.8.
      • Category agreement (F1): 0.474098 to 0.843334 (4 checks)
      • Matching records (F1): 0.952125 to 0.984765 (12 checks)
      • Numerical agreement (CCC): 0.846923 to 0.919139 (4 checks)
      • Present, finite data cells (F1): 0.952125 to 0.984765 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.454821
      • member 2: 0.637024
      • member 3: 0.35463
      • member 4: 0.539119
  42. GPT-5.6 Sol / Open-ended code / run 1 → result 7 (spatial graphs)
    • Content: Content score below 0.80. Value: 0.773796. Required minimum: 0.8.
      • Matching records (F1): 0.904103 to 0.984765 (12 checks)
      • Numerical agreement (CCC): 0.998463 to 1 (8 checks)
      • Present, finite data cells (F1): 0.904103 to 0.984765 (8 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.704673
      • member 2: 0.787825
      • member 3: 0.715657
  43. GPT-5.6 Sol / Open-ended code / run 1 → result 8 (interactions)
    • Content: Content score below 0.80. Value: 0.692221. Required minimum: 0.8.
      • Matching records (F1): 0.952125 to 0.984765 (4 checks)
      • Numerical agreement (CCC): 0.4594 to 0.980242 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.47387
      • member 2: 0.445355
  44. GPT-5.6 Sol / Open-ended code / run 1 → result 9 (neighborhood enrichment)
    • Content: Content score below 0.80. Value: 0.726274. Required minimum: 0.8.
      • Matching records (F1): 0.952125 to 0.984765 (4 checks)
      • Numerical agreement (CCC): 0.521771 to 0.976098 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.513822
      • member 2: 0.533706
    • Check: A required check is below its minimum. Required minimum: 0.9.
      • Numerical agreement (CCC): 0.521771 to 0.550537 (2 checks)
  45. GPT-5.6 Sol / Open-ended code / run 2 → result 1 (illumination)
    • Content: Content score below 0.80. Value: 0.623891. Required minimum: 0.8.
      • Required fields: 0.455009 to 0.95546 (20 checks)
  46. GPT-5.6 Sol / Open-ended code / run 2 → result 3 (core images)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Image agreement: 0 to 0.982303 (12 checks)
      • Numerical agreement (CCC): 0 (4 checks)
      • Required content missing or unreadable: 0 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  47. GPT-5.6 Sol / Open-ended code / run 2 → result 4 (nuclear masks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.759733
      • member 2: 0.793621
  48. GPT-5.6 Sol / Open-ended code / run 2 → result 5 (cell measurements)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0.94868 to 0.979313 (8 checks)
      • Numerical agreement (CCC): 0.872478 to 0.943199 (8 checks)
      • Present, finite data cells (F1): 0.94868 to 0.979313 (8 checks)
      • Required content missing or unreadable: 0 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  49. GPT-5.6 Sol / Open-ended code / run 2 → result 6 (phenotypes)
    • Content: Content score below 0.80. Value: 0.750607. Required minimum: 0.8.
      • Category agreement (F1): 0.815919 to 0.935148 (4 checks)
      • Matching records (F1): 0.94868 to 0.979313 (12 checks)
      • Numerical agreement (CCC): 0.963822 to 0.983906 (4 checks)
      • Present, finite data cells (F1): 0.94868 to 0.979313 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.744728
      • member 2: 0.723319
      • member 3: 0.698925
  50. GPT-5.6 Sol / Open-ended code / run 2 → result 7 (spatial graphs)
    • Content: Content score below 0.80. Value: 0.773047. Required minimum: 0.8.
      • Matching records (F1): 0.897158 to 0.979313 (12 checks)
      • Numerical agreement (CCC): 0.998594 to 1 (8 checks)
      • Present, finite data cells (F1): 0.897158 to 0.979313 (8 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.686345
      • member 2: 0.715132
  51. GPT-5.6 Sol / Open-ended code / run 3 → result 3 (core images)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Image agreement: 0 to 0.984012 (12 checks)
      • Numerical agreement (CCC): 0 (4 checks)
      • Required content missing or unreadable: 0 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  52. GPT-5.6 Sol / Open-ended code / run 3 → result 4 (nuclear masks)
    • Content: Content score below 0.80. Value: 0.795897. Required minimum: 0.8.
      • Image agreement: 0.801181 to 0.965615 (8 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.755741
      • member 2: 0.780239
  53. GPT-5.6 Sol / Open-ended code / run 3 → result 5 (cell measurements)
    • Content: Content score below 0.80. Value: 0.701464. Required minimum: 0.8.
      • Matching records (F1): 0.93352 to 0.97058 (12 checks)
      • Numerical agreement (CCC): 0.967283 to 0.996113 (12 checks)
      • Present, finite data cells (F1): 0.923653 to 0.97058 (12 checks)
      • Required fields: 0.989691 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.787115
      • member 2: 0.620867
      • member 3: 0.728622
      • member 4: 0.669251
  54. GPT-5.6 Sol / Open-ended code / run 3 → result 6 (phenotypes)
    • Content: Content score below 0.80. Value: 0.622344. Required minimum: 0.8.
      • Category agreement (F1): 0.724487 to 0.94216 (4 checks)
      • Matching records (F1): 0.93352 to 0.97058 (12 checks)
      • Numerical agreement (CCC): 0.606127 to 0.972951 (4 checks)
      • Present, finite data cells (F1): 0.93352 to 0.97058 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.798056
      • member 2: 0.684697
      • member 3: 0.562033
      • member 4: 0.444589
  55. GPT-5.6 Sol / Open-ended code / run 3 → result 7 (spatial graphs)
    • Content: Content score below 0.80. Value: 0.732471. Required minimum: 0.8.
      • Matching records (F1): 0.900423 to 0.97058 (12 checks)
      • Numerical agreement (CCC): 0.998604 to 1 (8 checks)
      • Present, finite data cells (F1): 0.900423 to 0.97058 (8 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.662134
      • member 2: 0.76031
      • member 3: 0.690968
  56. DeepSeek V4 Pro / Galaxy-API code / run 3 → result 6 (phenotypes)
    • Content: Content score below 0.80. Value: 0.276984. Required minimum: 0.8.
      • Category agreement (F1): 0.40673 to 0.744003 (4 checks)
      • Numerical agreement (CCC): 0.364874 to 0.599745 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.243934
      • member 2: 0.445806
      • member 3: 0.236346
      • member 4: 0.181851
  57. DeepSeek V4 Pro / Galaxy-API code / run 3 → result 8 (interactions)
    • Content: Content score below 0.80. Value: 0.453127. Required minimum: 0.8.
      • Numerical agreement (CCC): 0.161442 to 0.828215 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.161442
      • member 2: 0.285264
      • member 3: 0.537589
  58. DeepSeek V4 Pro / Galaxy-API code / run 3 → result 9 (neighborhood enrichment)
    • Content: Content score below 0.80. Value: 0.533581. Required minimum: 0.8.
      • Numerical agreement (CCC): 0.341855 to 0.851853 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0.341855
      • member 2: 0.459218
      • member 3: 0.481399
    • Check: A required check is below its minimum. Required minimum: 0.9.
      • Numerical agreement (CCC): 0.341855 to 0.851853 (4 checks)
  59. DeepSeek V4 Pro / Open-ended code / run 1 → result 1 (illumination)
    • Content: Content score below 0.80. Value: 0.0529719. Required minimum: 0.8.
      • Required fields: 0.0543108 to 0.516892 (20 checks)
  60. DeepSeek V4 Pro / Open-ended code / run 1 → result 2 (registered images)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Image agreement: 0
      • Numerical agreement (CCC): 0
  61. DeepSeek V4 Pro / Open-ended code / run 1 → result 3 (core images)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Image agreement: 0 to 0.866195 (12 checks)
      • Numerical agreement (CCC): 0 (4 checks)
      • Required content missing or unreadable: 0 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  62. DeepSeek V4 Pro / Open-ended code / run 1 → result 4 (nuclear masks)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Image agreement: 0 to 0.187859 (8 checks)
      • Required content missing or unreadable: 0 (3 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0.00672086
      • member 4: 0
  63. DeepSeek V4 Pro / Open-ended code / run 1 → result 5 (cell measurements)
    • Content: Content score below 0.80. Value: 5.85897e-12. Required minimum: 0.8.
      • Matching records (F1): 0 to 0.0529423 (12 checks)
      • Numerical agreement (CCC): 0 to 0.999988 (12 checks)
      • Present, finite data cells (F1): 0 to 0.0529423 (12 checks)
      • Required fields: 0.0784314 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 2.34359e-11
      • member 4: 0
  64. DeepSeek V4 Pro / Open-ended code / run 1 → result 6 (phenotypes)
    • Content: Content score below 0.80. Value: 1.54105e-07. Required minimum: 0.8.
      • Category agreement (F1): 0 to 0.135924 (4 checks)
      • Matching records (F1): 0 to 0.0529423 (12 checks)
      • Numerical agreement (CCC): 0 to 0.577257 (4 checks)
      • Present, finite data cells (F1): 0 to 0.0529423 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 6.16418e-07
      • member 4: 0
  65. DeepSeek V4 Pro / Open-ended code / run 1 → result 7 (spatial graphs)
    • Content: Content score below 0.80. Value: 9.90515e-09. Required minimum: 0.8.
      • Matching records (F1): 0 to 0.0529423 (12 checks)
      • Numerical agreement (CCC): 0 to 0.999988 (8 checks)
      • Present, finite data cells (F1): 0 to 0.0529423 (8 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 3.96206e-08
      • member 4: 0
  66. DeepSeek V4 Pro / Open-ended code / run 1 → result 8 (interactions)
    • Content: Content score below 0.80. Value: 0.00519521. Required minimum: 0.8.
      • Matching records (F1): 0 to 0.882759 (5 checks)
      • Numerical agreement (CCC): 0.339707 to 0.407947 (4 checks)
      • Present, finite data cells (F1): 0.882759
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0.0207808
      • member 4: 0
  67. DeepSeek V4 Pro / Open-ended code / run 1 → result 9 (neighborhood enrichment)
    • Content: Content score below 0.80. Value: 0.00271358. Required minimum: 0.8.
      • Category agreement (F1): 0.748447 (2 checks)
      • Matching records (F1): 0 to 0.882759 (5 checks)
      • Numerical agreement (CCC): 0.0635228 to 0.27478 (4 checks)
      • Present, finite data cells (F1): 0.882759 to 0.996904 (3 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0.0108543
      • member 4: 0
    • Check: A required check is below its minimum. Required minimum: 0.9.
      • Numerical agreement (CCC): 0.0635228 to 0.27478 (4 checks)
  68. DeepSeek V4 Pro / Open-ended code / run 2 → result 1 (illumination)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (20 checks)
      • Required fields: 0 (40 checks)
    • Instruction: Required file is missing: 01_illumination/exemplar-002-cycle-01.ome.tiff/flatfield.tiffTask requirement: 1. final_answer/01_illumination/ TIFF flatfield.tiff and darkfield.tiff for each input cycle, preserving all channels; {cycle} is the input cycle file name. Files: {cycle}/flatfield.tiff, {cycle}/darkfield.tiff.
    • Instruction: Required file is missing: 01_illumination/exemplar-002-cycle-01.ome.tiff/darkfield.tiffTask requirement: 1. final_answer/01_illumination/ TIFF flatfield.tiff and darkfield.tiff for each input cycle, preserving all channels; {cycle} is the input cycle file name. Files: {cycle}/flatfield.tiff, {cycle}/darkfield.tiff.
    • Instruction: Required file is missing: 01_illumination/exemplar-002-cycle-02.ome.tiff/flatfield.tiffTask requirement: 1. final_answer/01_illumination/ TIFF flatfield.tiff and darkfield.tiff for each input cycle, preserving all channels; {cycle} is the input cycle file name. Files: {cycle}/flatfield.tiff, {cycle}/darkfield.tiff.
    • Instruction: Required file is missing: 01_illumination/exemplar-002-cycle-02.ome.tiff/darkfield.tiffTask requirement: 1. final_answer/01_illumination/ TIFF flatfield.tiff and darkfield.tiff for each input cycle, preserving all channels; {cycle} is the input cycle file name. Files: {cycle}/flatfield.tiff, {cycle}/darkfield.tiff.
    • Instruction: Required file is missing: 01_illumination/exemplar-002-cycle-03.ome.tiff/flatfield.tiffTask requirement: 1. final_answer/01_illumination/ TIFF flatfield.tiff and darkfield.tiff for each input cycle, preserving all channels; {cycle} is the input cycle file name. Files: {cycle}/flatfield.tiff, {cycle}/darkfield.tiff.
    • Instruction: Required file is missing: 01_illumination/exemplar-002-cycle-03.ome.tiff/darkfield.tiffTask requirement: 1. final_answer/01_illumination/ TIFF flatfield.tiff and darkfield.tiff for each input cycle, preserving all channels; {cycle} is the input cycle file name. Files: {cycle}/flatfield.tiff, {cycle}/darkfield.tiff.
    • Instruction: Required file is missing: 01_illumination/exemplar-002-cycle-04.ome.tiff/flatfield.tiffTask requirement: 1. final_answer/01_illumination/ TIFF flatfield.tiff and darkfield.tiff for each input cycle, preserving all channels; {cycle} is the input cycle file name. Files: {cycle}/flatfield.tiff, {cycle}/darkfield.tiff.
    • Instruction: Required file is missing: 01_illumination/exemplar-002-cycle-04.ome.tiff/darkfield.tiffTask requirement: 1. final_answer/01_illumination/ TIFF flatfield.tiff and darkfield.tiff for each input cycle, preserving all channels; {cycle} is the input cycle file name. Files: {cycle}/flatfield.tiff, {cycle}/darkfield.tiff.
    • Instruction: Required file is missing: 01_illumination/exemplar-002-cycle-05.ome.tiff/flatfield.tiffTask requirement: 1. final_answer/01_illumination/ TIFF flatfield.tiff and darkfield.tiff for each input cycle, preserving all channels; {cycle} is the input cycle file name. Files: {cycle}/flatfield.tiff, {cycle}/darkfield.tiff.
    • Instruction: Required file is missing: 01_illumination/exemplar-002-cycle-05.ome.tiff/darkfield.tiffTask requirement: 1. final_answer/01_illumination/ TIFF flatfield.tiff and darkfield.tiff for each input cycle, preserving all channels; {cycle} is the input cycle file name. Files: {cycle}/flatfield.tiff, {cycle}/darkfield.tiff.
    • Instruction: Required file is missing: 01_illumination/exemplar-002-cycle-06.ome.tiff/flatfield.tiffTask requirement: 1. final_answer/01_illumination/ TIFF flatfield.tiff and darkfield.tiff for each input cycle, preserving all channels; {cycle} is the input cycle file name. Files: {cycle}/flatfield.tiff, {cycle}/darkfield.tiff.
    • Instruction: Required file is missing: 01_illumination/exemplar-002-cycle-06.ome.tiff/darkfield.tiffTask requirement: 1. final_answer/01_illumination/ TIFF flatfield.tiff and darkfield.tiff for each input cycle, preserving all channels; {cycle} is the input cycle file name. Files: {cycle}/flatfield.tiff, {cycle}/darkfield.tiff.
    • Instruction: Required file is missing: 01_illumination/exemplar-002-cycle-07.ome.tiff/flatfield.tiffTask requirement: 1. final_answer/01_illumination/ TIFF flatfield.tiff and darkfield.tiff for each input cycle, preserving all channels; {cycle} is the input cycle file name. Files: {cycle}/flatfield.tiff, {cycle}/darkfield.tiff.
    • Instruction: Required file is missing: 01_illumination/exemplar-002-cycle-07.ome.tiff/darkfield.tiffTask requirement: 1. final_answer/01_illumination/ TIFF flatfield.tiff and darkfield.tiff for each input cycle, preserving all channels; {cycle} is the input cycle file name. Files: {cycle}/flatfield.tiff, {cycle}/darkfield.tiff.
    • Instruction: Required file is missing: 01_illumination/exemplar-002-cycle-08.ome.tiff/flatfield.tiffTask requirement: 1. final_answer/01_illumination/ TIFF flatfield.tiff and darkfield.tiff for each input cycle, preserving all channels; {cycle} is the input cycle file name. Files: {cycle}/flatfield.tiff, {cycle}/darkfield.tiff.
    • Instruction: Required file is missing: 01_illumination/exemplar-002-cycle-08.ome.tiff/darkfield.tiffTask requirement: 1. final_answer/01_illumination/ TIFF flatfield.tiff and darkfield.tiff for each input cycle, preserving all channels; {cycle} is the input cycle file name. Files: {cycle}/flatfield.tiff, {cycle}/darkfield.tiff.
    • Instruction: Required file is missing: 01_illumination/exemplar-002-cycle-09.ome.tiff/flatfield.tiffTask requirement: 1. final_answer/01_illumination/ TIFF flatfield.tiff and darkfield.tiff for each input cycle, preserving all channels; {cycle} is the input cycle file name. Files: {cycle}/flatfield.tiff, {cycle}/darkfield.tiff.
    • Instruction: Required file is missing: 01_illumination/exemplar-002-cycle-09.ome.tiff/darkfield.tiffTask requirement: 1. final_answer/01_illumination/ TIFF flatfield.tiff and darkfield.tiff for each input cycle, preserving all channels; {cycle} is the input cycle file name. Files: {cycle}/flatfield.tiff, {cycle}/darkfield.tiff.
    • Instruction: Required file is missing: 01_illumination/exemplar-002-cycle-10.ome.tiff/flatfield.tiffTask requirement: 1. final_answer/01_illumination/ TIFF flatfield.tiff and darkfield.tiff for each input cycle, preserving all channels; {cycle} is the input cycle file name. Files: {cycle}/flatfield.tiff, {cycle}/darkfield.tiff.
    • Instruction: Required file is missing: 01_illumination/exemplar-002-cycle-10.ome.tiff/darkfield.tiffTask requirement: 1. final_answer/01_illumination/ TIFF flatfield.tiff and darkfield.tiff for each input cycle, preserving all channels; {cycle} is the input cycle file name. Files: {cycle}/flatfield.tiff, {cycle}/darkfield.tiff.
  69. DeepSeek V4 Pro / Open-ended code / run 2 → result 2 (registered images)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Image agreement: 0
      • Numerical agreement (CCC): 0
  70. DeepSeek V4 Pro / Open-ended code / run 2 → result 3 (core images)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Image agreement: 0 to 0.715182 (12 checks)
      • Numerical agreement (CCC): 0 (4 checks)
      • Required content missing or unreadable: 0 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  71. DeepSeek V4 Pro / Open-ended code / run 2 → result 4 (nuclear masks)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Image agreement: 0 (8 checks)
      • Required content missing or unreadable: 0 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  72. DeepSeek V4 Pro / Open-ended code / run 2 → result 5 (cell measurements)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0 (12 checks)
      • Numerical agreement (CCC): 0 (12 checks)
      • Present, finite data cells (F1): 0 (12 checks)
      • Required fields: 0.989691 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  73. DeepSeek V4 Pro / Open-ended code / run 2 → result 6 (phenotypes)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Category agreement (F1): 0 (4 checks)
      • Matching records (F1): 0 (12 checks)
      • Numerical agreement (CCC): 0 (4 checks)
      • Present, finite data cells (F1): 0 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  74. DeepSeek V4 Pro / Open-ended code / run 2 → result 7 (spatial graphs)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0 (12 checks)
      • Numerical agreement (CCC): 0 (8 checks)
      • Present, finite data cells (F1): 0 (8 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  75. DeepSeek V4 Pro / Open-ended code / run 2 → result 8 (interactions)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0 to 0.882759 (8 checks)
      • Numerical agreement (CCC): 0.115231 to 0.448953 (4 checks)
      • Present, finite data cells (F1): 0.882759 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  76. DeepSeek V4 Pro / Open-ended code / run 2 → result 9 (neighborhood enrichment)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0 to 0.882759 (8 checks)
      • Numerical agreement (CCC): 0.103762 to 0.379389 (4 checks)
      • Present, finite data cells (F1): 0.882759 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
    • Check: A required check is below its minimum. Required minimum: 0.9.
      • Numerical agreement (CCC): 0.103762 to 0.379389 (4 checks)
  77. DeepSeek V4 Pro / Open-ended code / run 3 → result 1 (illumination)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Required content missing or unreadable: 0 (20 checks)
      • Required fields: 0 (40 checks)
  78. DeepSeek V4 Pro / Open-ended code / run 3 → result 2 (registered images)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Image agreement: 0
      • Numerical agreement (CCC): 0
  79. DeepSeek V4 Pro / Open-ended code / run 3 → result 3 (core images)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Image agreement: 0 to 0.819323 (12 checks)
      • Numerical agreement (CCC): 0 (4 checks)
      • Required content missing or unreadable: 0 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  80. DeepSeek V4 Pro / Open-ended code / run 3 → result 4 (nuclear masks)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Image agreement: 0 (8 checks)
      • Required content missing or unreadable: 0 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  81. DeepSeek V4 Pro / Open-ended code / run 3 → result 5 (cell measurements)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0 (12 checks)
      • Numerical agreement (CCC): 0 (12 checks)
      • Present, finite data cells (F1): 0 (12 checks)
      • Required fields: 0.923077 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  82. DeepSeek V4 Pro / Open-ended code / run 3 → result 6 (phenotypes)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Category agreement (F1): 0 (4 checks)
      • Matching records (F1): 0 (12 checks)
      • Numerical agreement (CCC): 0 (4 checks)
      • Present, finite data cells (F1): 0 (4 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  83. DeepSeek V4 Pro / Open-ended code / run 3 → result 7 (spatial graphs)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0 (12 checks)
      • Numerical agreement (CCC): 0 (8 checks)
      • Present, finite data cells (F1): 0 (8 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  84. DeepSeek V4 Pro / Open-ended code / run 3 → result 8 (interactions)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0 to 0.882759 (6 checks)
      • Numerical agreement (CCC): 0 to 0.256976 (4 checks)
      • Present, finite data cells (F1): 0.753846 to 0.882759 (2 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
  85. DeepSeek V4 Pro / Open-ended code / run 3 → result 9 (neighborhood enrichment)
    • Content: Content score below 0.80. Value: 0. Required minimum: 0.8.
      • Matching records (F1): 0 to 0.882759 (6 checks)
      • Numerical agreement (CCC): 0.0258203 to 0.0925708 (4 checks)
      • Present, finite data cells (F1): 0.753846 to 0.882759 (2 checks)
    • Member: A required member scores below 0.80. Required minimum: 0.8.
      • member 1: 0
      • member 2: 0
      • member 3: 0
      • member 4: 0
    • Check: A required check is below its minimum. Required minimum: 0.9.
      • Numerical agreement (CCC): 0.0258203 to 0.0925708 (4 checks)

Task text

The scientific part of the task, identical in both conditions. The general submission rules and the instructions for each condition are on the overview page.

Full task text

Task

Analyze ten multiplex-imaging cycles and four tissue cores to quantify cells, assign phenotypes and characterize within-core neighborhoods. Preserve all supplied channels and cores; these cores are not biological replicates and do not support clinical or between-group claims. Derive nuclear instances and per-cell marker measurements from registered multiplex images. Use marker-intensity mixture modeling with the supplied phenotype rules, retaining uncertain assignments. Test spatial phenotype association against within-core label permutations; cells are spatial observations, not independent biological replicates.

Inputs

  • All ten imaging cycles, four-core identity information and channel/cycle metadata.
  • The supplied marker and phenotype definitions and image calibration.

Key parameters and conditions

  • Estimate illumination by retrospective low-rank plus sparse decomposition into flat-field and dark-field components, solved with the original inexact augmented-Lagrangian scheme on the per-pixel intensity-sorted tile stack with fixed absolute smoothness weights of 0.1 (flat field) and 0.01 (dark field) rather than data-derived weights. Stitch tiles and register imaging cycles jointly using phase-correlation alignments organized by tile adjacency and a spanning tree. Detect TMA cores with a pretrained UNet probability map of the downsampled DNA channel, locating core centers and using active contours for core masks. Use alignment channel 0/max shift 30 and core-detection channel 0/downsampling 5/sensitivity 0.3/buffer 2. Preserve mask-label–CellID linkage, centroid coordinates and all channels; integer mask labels are arbitrary.
  • Segment nuclei with a model pretrained on multiplex fluorescence images from diverse tissues, predicting nuclear-center/distance and interior maps followed by deep watershed. Use nuclear channel 0 at 0.65 µm/pixel, center-maxima threshold 0.1 and interior threshold 0.2. Do not expand nuclear masks into whole-cell masks. Measure mean marker intensity and morphological/spatial properties within each labeled nucleus, preserving CellID and centroid coordinates.
  • Retain all cells and markers, including DNA channels, with raw intensities and natural-log(1+x) values. For each core use automatic marker gating by a two-component intensity mixture: clip each raw marker at its 0.01st/99.99th percentiles for the gate fit, apply log1p once, fit a two-component Gaussian mixture (seed 0), and use the midpoint of its two means as the gate. Rescale log1p raw marker values to [0,1] with the gate at 0.5, then apply the supplied phenotype rules. Use raw intensities, not already logged X, as the source for gating and rescaling. Do not subsample or replace the rules with manual gates.
  • Within each core, build a radius-46 graph in the untransformed generic core-image pixel coordinates, without self-loops or cross-core edges. Compute unweighted row-normalized phenotype interaction and neighborhood enrichment with 1,000 permutations/seed 0. Retain counts and z-scores including undefined values; they are not p-values. Do not rescale coordinates to infer a physical radius.
  • Deep-watershed postprocessing uses maxima radius 1 pixel, interior smoothing 2 pixels and minimum object/hole area 15 pixels. Keep unresolved phenotypes as Unknown. Store each image or mask as one TIFF series. Rescale log1p intensity piecewise linearly: [minimum, gate] to [0, 0.5] and [gate, maximum] to [0.5, 1].

Required results

  1. final_answer/01_illumination/
    TIFF
    flatfield.tiff and darkfield.tiff for each input cycle, preserving all channels; {cycle} is the input cycle file name. Files: {cycle}/flatfield.tiff, {cycle}/darkfield.tiff.
  2. final_answer/02_registered_images/
    OME-TIFF
    registered.ome.tiff: complete registered multichannel image with spatial/channel metadata. Files: registered.ome.tiff.
  3. final_answer/03_core_images/{core}/
    OME-TIFF + TIFF
    image.ome.tiff and mask.tiff for each of the four extracted cores, with all channels and extraction masks. {core} numbers the four cores 1–4 in row-major order of their positions in the registered image (top-left, top-right, bottom-left, bottom-right); use the same numbers in every result. Files: image.ome.tiff, mask.tiff.
  4. final_answer/04_nuclear_masks/{core}.tiff
    TIFF labeled mask
    Complete nuclear labels and segmentation diagnostics.
  5. final_answer/05_cell_measurements/{core}.csv
    CSV + H5AD
    The measurement CSV and a same-core .h5ad with log1p marker matrix X, raw intensities in raw/X and their identities in raw/var. CSV/H5AD preserve CellID, X_centroid, Y_centroid and every measured marker. Files: {core}.csv, {core}.h5ad.
  6. final_answer/06_phenotypes/{core}/
    H5AD
    Phenotypes with complete measurements and identity linkage. Use CellID as observation identity, categorical obs/phenotype and rescaled marker X; retain raw intensities. Files: cells.h5ad.
  7. final_answer/07_spatial_graphs/{core}/
    H5AD
    Within-core connectivity and coordinate/identity metadata. Store obsm/spatial and obsp/spatial_connectivities, obsp/spatial_distances. Files: cells.h5ad.
  8. final_answer/08_interactions/{core}/
    H5AD
    Unweighted row-normalized phenotype interactions. Store the phenotype-labelled matrix in uns/phenotype_interactions, ordered by obs/phenotype categories. Files: cells.h5ad.
  9. final_answer/09_neighborhood_enrichment/{core}/
    H5AD
    Complete enrichment counts and z-scores with phenotype labels and undefined entries. Store count and zscore matrices in uns/phenotype_nhood_enrichment, ordered by obs/phenotype categories. Files: cells.h5ad.

How this task is scored

Each scored result is compared with the reference result, which the task authors made by running the IWC workflow behind this task on usegalaxy.org with the settings in the task text. A result's score is the product of the checks listed for it, each from 0 to 1. When a result is scored per sample or other unit, each copy gets its own score and the result's score is their average; if any copy is missing or cannot be read, the result scores 0. A passing result must score at least 0.80 and meet the required member checks, method and output instructions. A failing result retains its numerical score in the continuous average. The overview page describes the checks in more detail.

No.Required resultWhat the task asks for How it is scored
101_illumination/
TIFF		flatfield.tiff and darkfield.tiff for each input cycle, preserving all channels; {cycle} is the input cycle file name. Files: {cycle}/flatfield.tiff, {cycle}/darkfield.tiff.
  • the same nonzero pixels with agreeing intensities (F1 and concordance correlation)
Scored for each of the 10 imaging cycles and averaged.
202_registered_images/
OME-TIFF		registered.ome.tiff: complete registered multichannel image with spatial/channel metadata. Files: registered.ome.tiff.
  • the same nonzero pixels with agreeing intensities (F1 and concordance correlation)
303_core_images/{core}/
OME-TIFF + TIFF		image.ome.tiff and mask.tiff for each of the four extracted cores, with all channels and extraction masks. {core} numbers the four cores 1–4 in row-major order of their positions in the registered image (top-left, top-right, bottom-left, bottom-right); use the same numbers in every result. Files: image.ome.tiff, mask.tiff.
  • the same nonzero pixels with agreeing intensities (F1 and concordance correlation)
  • the same foreground and matching objects (F1)
Scored for each of the 4 tissue cores and averaged.
404_nuclear_masks/{core}.tiff
TIFF labeled mask		Complete nuclear labels and segmentation diagnostics.
  • the same foreground and matching objects (F1)
Scored for each of the 4 tissue cores and averaged.
505_cell_measurements/{core}.csv
CSV + H5AD		The measurement CSV and a same-core .h5ad with log1p marker matrix X, raw intensities in raw/X and their identities in raw/var. CSV/H5AD preserve CellID, X_centroid, Y_centroid and every measured marker. Files: {core}.csv, {core}.h5ad.
  • the same rows or records as the reference (F1 of their identifiers)
  • the required columns or fields are present (F1)
  • values are present in the same cells (F1)
  • values agree (Lin's concordance correlation)
Scored for each of the 4 tissue cores and averaged.
606_phenotypes/{core}/
H5AD		Phenotypes with complete measurements and identity linkage. Use CellID as observation identity, categorical obs/phenotype and rescaled marker X; retain raw intensities. Files: cells.h5ad.
  • the same rows or records as the reference (F1 of their identifiers)
  • the required columns or fields are present (F1)
  • values are present in the same cells (F1)
  • values agree (Lin's concordance correlation)
  • category labels agree (macro F1)
Scored for each of the 4 tissue cores and averaged.
707_spatial_graphs/{core}/
H5AD		Within-core connectivity and coordinate/identity metadata. Store obsm/spatial and obsp/spatial_connectivities, obsp/spatial_distances. Files: cells.h5ad.
  • the same rows or records as the reference (F1 of their identifiers)
  • the required columns or fields are present (F1)
  • values are present in the same cells (F1)
  • values agree (Lin's concordance correlation)
Scored for each of the 4 tissue cores and averaged.
808_interactions/{core}/
H5AD		Unweighted row-normalized phenotype interactions. Store the phenotype-labelled matrix in uns/phenotype_interactions, ordered by obs/phenotype categories. Files: cells.h5ad.
  • the same rows or records as the reference (F1 of their identifiers)
  • the required columns or fields are present (F1)
  • values are present in the same cells (F1)
  • values agree (Lin's concordance correlation)
  • category labels agree (macro F1)
Scored for each of the 4 tissue cores and averaged.
909_neighborhood_enrichment/{core}/
H5AD		Complete enrichment counts and z-scores with phenotype labels and undefined entries. Store count and zscore matrices in uns/phenotype_nhood_enrichment, ordered by obs/phenotype categories. Files: cells.h5ad.
  • the same rows or records as the reference (F1 of their identifiers)
  • the required columns or fields are present (F1)
  • values are present in the same cells (F1)
  • values agree (Lin's concordance correlation)
  • category labels agree (macro F1)
Scored for each of the 4 tissue cores and averaged.

Data updated 27 October 2026, 08:48 EDT.