Pipeline

Scanpy

Scanpy cell-type annotation pipeline reported in the primary table; fitting/configuration details unextracted.

Overview

Scanpy cell-type annotation pipeline reported in the primary table; fitting/configuration details unextracted.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

2 evaluations · 2 metric rows. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Pipeline: Scanpy	Protocol: scFoundation cell-type annotation comparison Segerstolpe: Segerstolpe cell-type annotation Dataset subset: Segerstolpe subset used in scFoundation Supplementary Table4 (scFoundation cell-type annotation comparison split)	0.540 macro_f1 fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · source checked Methods, coverage and source Scanpy on scFoundation cell-type annotation comparison Segerstolpe: Segerstolpe cell-type annotation Cell-type annotation evaluated by unweighted mean of cell-type F1 scores. Each class F1=TP/(TP+0.5*(FP+FN)), defined in Supplementary Note3. Exact dataset release, split manifest, fitting and preprocessing remain unextracted. Aggregation: Not reported scFoundation primary supplement, Table4 · Supplementary Table4, PDF p16, row Scanpy, column Segerstolpe
Pipeline: Scanpy	Protocol: scFoundation cell-type annotation comparison Zheng68K: Zheng68K cell-type annotation Dataset subset: Zheng68K subset used in scFoundation Supplementary Table4 (scFoundation cell-type annotation comparison split)	0.547 macro_f1 fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · source checked Methods, coverage and source Scanpy on scFoundation cell-type annotation comparison Zheng68K: Zheng68K cell-type annotation Cell-type annotation evaluated by unweighted mean of cell-type F1 scores. Each class F1=TP/(TP+0.5*(FP+FN)), defined in Supplementary Note3. Exact dataset release, split manifest, fitting and preprocessing remain unextracted. Aggregation: Not reported scFoundation primary supplement, Table4 · Supplementary Table4, PDF p16, row Scanpy, column Zheng68K

Source checking is not independent reproduction. Release 2026-09-23-2b89723c6dd9.

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Evidence

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Evidence table

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