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Unify traditional and new pipeline#1

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afermg wants to merge 68 commits intocellposefrom
unify
Closed

Unify traditional and new pipeline#1
afermg wants to merge 68 commits intocellposefrom
unify

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@afermg afermg commented Dec 4, 2024 •
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This PR enables the usage of the same pipeline for yeast and arbitrary experiments. The additional features added to aliby are:

cellpose segmentation
cellpose stitch3D tracking
cp_measure (CellProfiler) features
output to parquet tables

swainlab and others added 30 commits June 7, 2024 14:44
@swainlab
change(pipeline): extractor params can be set
87751d1
@swainlab
refactor(traps): deleted unnecessary code
40f0dd8
@swainlab
change:tile_size defined only in global_parameters
1f18f39
@swainlab
change(tiler): added magnification
7865490 
If magnification differs from the default, re-scale tile_size and
parameters for segmenting traps.
@swainlab
tidy: metadata; created metadata_legacy
d88f4e7
@swainlab
change: in process, converting metadata
288ac2c
@swainlab
change: tidied metadata
f814442 
Removed OMERO_channels and spatial_positions from pipeline.py
@swainlab
added default outline fns to global_parameters
d0e03c6
@swainlab
change: global_parameters -> global_settings
9c44c5d
@swainlab
feature: positions allowed different signals
d26e55d 
Works for legacy log files only; no examples yet of new log file.
@swainlab
change(grouped): added all_available
98d342c
@afermg
fix(pipe): specify Image from wildcard
ce9405a
@afermg
fix(extractor): support regionprops_table feats
f01b32d
@swainlab
change(grouper): removed annoying tqdm
b4d4c8d
@swainlab
fix(metadata_legacy): wrong type in time_settings
2c32933 
time_settings/ntimepoints should be int not List[int].
@swainlab
change: added total_squared to cell.py
f451a32 
Necessary to calculate the noise for the mother and bud.
@swainlab
change: remove total and total_squared as defaults
fb06b86
@swainlab
feature(PipelineParameters): channels in general
60cf9aa 
channels can can be specified in the general dict, overriding OMERO
@afermg
deps: upgrade pytorch for compat w cellprofiler-library
391176c
@afermg
[WIP]feat: add support for cp_measure
3ca88e8
@afermg
feat: CellProf compat, cleanup, functools
0bb5fce 
Many improvements needed for CellProfiler features compatibility
- functools used to load functions dynamically
- support selecting channels numerically
- remove custom functions (these were never used)
- support metrics that return multiple results as a dictionary
@swainlab
change: add global_settings.default_time_interval
ff2fc89
@swainlab
refactor: split dynamic_writer from writer
e97674e
@swainlab
fix(signal): error in cols_to_mins
96fc944 
Missing brackets were giving non-monotonic time values.
@swainlab
change: no obligatory run method in ProcessABC
38ed8ac
@swainlab
change(pipeline): tps redefined if too large
40ca259
@swainlab
change: created tiles; traps -> process_traps
4796a12
@swainlab
change(bridge): added docs
36b2b71
@swainlab
change(grouper): prevent crash when signal missing
031639c 
Fixed signal to work on old legacy h5 files, where channels are stored differently.
@swainlab
change(examples): added run_zarr
ee15319
afermg added 20 commits January 20, 2025 19:28
@afermg
Merge branch 'remove_bottleneck' into unify
68a6083
@afermg
[WIP]feat: add new pipeline for Swain Lab experiments
ea0a223
@afermg
chore:Update dependencies
0ffafd4
@afermg
refactor: simplify segmenter dispatch
e80bf9f
@afermg
fix: update cp_measure wrapper
b54570d
@afermg
fix: add stitch3D to cellpose segmentation to silence warning
12a2fb0
@afermg
deps: relax cellpose version
6acd119
@afermg
deps: reintroduce pandas temporarily
227e3e5
@afermg
Merge branch 'parquet_pipeline' into reprocess_old_experiments
bb00e50
@afermg
fix(pipe): basic pipeline progresses in flavin experiments
b2cb034
@afermg
format: apply default ruff checks and fixes
6fdc5d7
@afermg
match latest changes upstream, follow ruff advice
c189d6c
@afermg
fix: non-baby runs post-simplification of repo
606c727
@afermg
fix(baby_client): ensure modelsets work
3d18157
@afermg
fix(baby_client): can instance baby again
60d4256
@afermg
deps: fix version to match alibylite
9db790f
@afermg
fix(baby_client): reach segmentation step in processing
dff37e5
@afermg
fix: baby pipeline runs again
ef84136 
[refactor]: Refactored segmenter and tracker dispatch functions to improve compatibility with Baby and Cellpose models, and added monkey patching for segmentation class to return masks only.
@afermg
fix(pipe): Both pipelines work properly
f635b22
@afermg
fix(extractor): cover fg calculation edge cases
6112576
@afermg afermg changed the title Unify Unify traditional and new pipeline Feb 17, 2025
@afermg afermg mentioned this pull request Feb 17, 2025
Closed
@afermg afermg closed this Nov 2, 2025
@afermg afermg deleted the unify branch November 2, 2025 15:51
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2 participants

@afermg @swainlab