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Start working on figures - #1401

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anwai98 merged 67 commits into
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paper-figures
Nov 13, 2026
Merged

Start working on figures#1401
anwai98 merged 67 commits into
devfrom
paper-figures

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@anwai98

@anwai98 anwai98 commented Oct 25, 2026

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Gonna keep this open as a knock for me!

@anwai98 anwai98 self-assigned this Oct 25, 2026
anwai98 and others added 22 commits November 1, 2026 12:12
@anwai98
Add the plotting scripts for Figures 2 and 3
994b9ea
@anwai98
Extend the evaluation baselines and merge the post-hoc figure scripts…
09094cd 
… into run_posthoc_scripts.py [skip ci]
@anwai98
Add a napari script to check the Platynereis time-lapse segmentation …
9c22955 
…and tracks [skip ci]
@anwai98
Add the cell-nucleus volume ratio script for the Platynereis time-lap…
4bcb41d 
…se [skip ci]
@anwai98
Add scripts for figure 1 architecture and workflow [skip ci]
ae3aa71
@anwai98
Add the whole slide panels of Figure 4 and the post-hoc classificatio…
d96022d 
…n script [skip ci]
@anwai98
Merge dev into paper-figures [skip ci]
5b2f6cf
@anwai98
Merge dev into paper-figures [skip ci]
75c23d5
@constantinpape
Update analysis scripts for Huisken data
94b5084
@constantinpape
Update huisken plotting scripts
7e76ac7
@anwai98
Add some more figure and other script changes [skip ci]
d3a4e55
@constantinpape
Add script for data size overview (#1409) [skip ci]
9e56ba4
@anwai98
Merge dev into paper-figures [skip ci]
cb802e6
@anwai98
Merge remote-tracking branch 'origin/paper-figures' into paper-figure…
21ecebb 
…s [skip ci]
@constantinpape
Update data overview scripts
3f1ca48
@anwai98
Update Figure 2 interactive OOD examples [skip ci]
5bdd5de
@anwai98
Format Figure 2 [skip ci]
849d5ca
@anwai98
Format Figure 4 [skip ci]
e22d874
@anwai98
Update Figure 6 datasets and EM nucleus evaluation [skip ci]
9817d9b
@anwai98
Add ilastik to Figure 4 [skip ci]
a68c62d
@anwai98
Apply Figure 4 feedback [skip ci]
be08f1c
@anwai98
Mark tuned EM baselines in Figure 6 [skip ci]
8c9dc42
@anwai98
anwai98 marked this pull request as ready for review November 5, 2026 15:31
anwai98 added 28 commits November 10, 2026 00:04
@anwai98
Rework Figure 1 after feedback: APG paths in panel a, dataset labels …
feb202c 
…and white cards in b, row names on the left in c, new spheroid, heart and Ki67 examples in d
@anwai98
Show Figure 5 panel b as pyramids: small error-dense windows of each …
2f20a8b 
…movie over its first frame, and fit the figure to A4
@anwai98
Use the new micro-sam2 logo in Figure 1
b15ecc0
@anwai98
Follow the codelore rules in the Figure 1 and 5 scripts and the track…
20b3095 
…ing evaluation
@anwai98
Sort the user study scripts into folders for the Huisken, Beghin and …
fa88118 
…Gruen labs
@anwai98
Add the exploration script for the Beghin lab EM data
03afa55
@anwai98
Rename the tracking evaluation and EM nucleus test set scripts and sh…
0e153a4 
…are the TMPDIR embedding patch from common
@anwai98
Rename the roots of the EM nucleus test sets in common
1cda316
@anwai98
Fold the tracking data conversion and the result collection into the …
927ef23 
…tracking evaluation, and the EM test set preparation into the EM preprocessing scripts
@anwai98
Drop the candidate label from the notes of the final EM nucleus test …
bcb5926 
…sets
@anwai98
Remove the UniSAM2 postprocessing sweep scripts from plotting
715c109
@anwai98
Pick dark or white mode labels on the bars by contrast in Figures 2, …
05bf561 
…3 and 5
@anwai98
Replace the EtchACell example of Figure 6 panel d with the Beghin lab…
09090a2 
… spheroid nuclei as panel e and widen the panel c legend
@anwai98
Segment the nuclei of the Beghin lab spheroid volume in 3d blocks, cl…
01d9905 
…ean them up and render the Figure 6 panel e views
@anwai98
Remove the untiled block option from the Beghin lab spheroid script
60df41c
@anwai98
Allow a tint per mode for the sub-bars of the automatic bar plots
b864cf2
@anwai98
Add the Extended Data 1 plots with all micro-sam2 model sizes
f16cc31
@anwai98
Add the Extended Data 2 plots of the micro-sam2 runtimes on CPU, GPU …
8cd8e2c 
…and Apple silicon
@anwai98
Add the micro-sam2 runtime benchmark for CPU, GPU and Apple silicon, …
7f8547a 
…with AIS timed on the APG embeddings
@anwai98
Show AIS and APG in Extended Data 1 and draw Extended Data 2 with sta…
e3e4862 
…cked part blocks for LIVECell and GoNuclear
@anwai98
Use log axes, per-slice minutes and wider bars in Extended Data 2, an…
ee494dd 
…d draw panel b like panel a
@anwai98
Limit the CPU CREMI APG B runtime benchmark to two volumes
b4d7882
@anwai98
Add the Apple M2 runtimes and empty the MPS cache between the benchma…
fab0ee5 
…rk samples
@anwai98
Use the M2 device tag in the Extended Data 2 axis and label sets
edf41cd
@anwai98
Load the committed device runtimes, mark modes not run and draw per-m…
6df7792 
…ethod legend cards in Extended Data 2 [skip ci]
@anwai98
Ignore the generated paper figures folder [skip ci]
6cc35d3
@anwai98
Read the M2 runtime tables from the benchmark folder instead of the r…
110a77a 
…epo [skip ci]
@anwai98
Rename the runtime benchmark script to runtime_benchmarking_script.py…
fa13ea4 
… and remove the Mac run script [skip ci]
@anwai98
anwai98 merged commit a3d35a4 into dev Nov 13, 2026
@anwai98
anwai98 deleted the paper-figures branch November 13, 2026 00:57
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@anwai98 @constantinpape