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fmi-basel
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gliberal-scMultipleX
Feature extraction and linking of multiplexing data.
BSD 3-Clause "New" or "Revised" License
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Refactor of organoid linking over multiplexing rounds
#72
nrepina
closed
1 year ago
2
Clean up config file parameters
#71
nrepina
closed
1 year ago
0
Refactor organoid linking
#70
nrepina
closed
1 year ago
0
Check for scikit-image version and apply the fix for centroid for version 0.20.0
#69
enricotagliavini
opened
1 year ago
0
Fractal task installation
#68
jluethi
closed
1 year ago
0
Fractal task adds duplicate columns
#67
jluethi
opened
1 year ago
0
New logging configuration
#66
enricotagliavini
closed
1 year ago
0
support multi channel images in centroid correction and migrate faim_hcs test to the new submodule namespace
#65
enricotagliavini
closed
1 year ago
1
Add neighbor analysis to FeatureExtraction.py
#64
nrepina
opened
1 year ago
1
Testing of different experiment settings
#63
nrepina
opened
1 year ago
0
Bundle FAIM_HCS
#62
enricotagliavini
closed
1 year ago
0
Improve feature wrapper and fractal task
#61
jluethi
closed
1 year ago
3
Extract morphology measurements only on segmentation channel.
#60
nrepina
closed
1 year ago
0
Cleanup the get_regionprops_measurements() function in feature_wrapper.py
#59
enricotagliavini
closed
1 year ago
3
Print summary at the end of nuc to mem linking
#58
enricotagliavini
opened
1 year ago
0
Switch to using Fractal get_regionprops_measurements for scMultiplex feature extraction
#57
nrepina
closed
1 year ago
2
Remove TODO.md?
#56
enricotagliavini
closed
1 year ago
1
Two Z centroids: scaled and unscaled
#55
nrepina
closed
1 year ago
0
Print scMultipleX version at the beginning of the run and fix typo
#54
enricotagliavini
closed
1 year ago
1
Check if output is correct of regionprops Z weighted_centroid
#53
nrepina
closed
1 year ago
1
Bundle faim_hcs v0.1.1?
#52
enricotagliavini
closed
1 year ago
0
Fix incomplete rows in Feature extraction
#51
enricotagliavini
closed
1 year ago
7
Change naming of Aspect Ration feature to be more specific
#50
nrepina
closed
1 year ago
0
[WIP] Fractal wrapper for scMultipleX
#49
jluethi
closed
1 year ago
8
Add version info to scMpx log file output
#48
nrepina
closed
1 year ago
0
Add illumination correction option
#47
nrepina
closed
1 year ago
0
More testing for 01 task parallelization
#46
enricotagliavini
opened
1 year ago
0
Clean up common config
#45
nrepina
closed
1 year ago
1
Parallelism fixes, implement proper exit codes and check for config files
#44
enricotagliavini
closed
1 year ago
0
Fix typos
#43
nrepina
closed
1 year ago
0
Check and error out if config file doesn't exists
#42
enricotagliavini
closed
1 year ago
1
Fix parallelization of tasks 04-07 to avoid race condition.
#41
nrepina
closed
1 year ago
0
Return non zero exit code when a Flow is no successful
#40
enricotagliavini
closed
1 year ago
1
Fix a few parallelism problems and logs
#39
enricotagliavini
closed
1 year ago
0
Roll back task 1 to thread-based parallelization.
#38
nrepina
closed
1 year ago
0
Add functionality to run parallel processes over arbitrary number of CPUs
#37
nrepina
closed
1 year ago
0
Find solution for failure of multiprocessing in task 02
#36
nrepina
closed
1 year ago
1
Switch to pty.fork() for subprocess cration to have full control over the I/O
#35
enricotagliavini
closed
1 year ago
0
Add a check for step dependencies ?
#34
enricotagliavini
opened
1 year ago
0
Added run_scmultiplex script to run all tasks in a single command.
#33
enricotagliavini
closed
1 year ago
0
Make --config option mandatory in all prefect scripts
#32
enricotagliavini
closed
1 year ago
0
Add support for cluster submission
#31
enricotagliavini
opened
1 year ago
0
Make separate logger for scmultiplex tasks
#30
nrepina
closed
1 year ago
2
Update feature extraction, aggregation, and task cleanup.
#29
nrepina
closed
1 year ago
0
Make surface area measurement optional
#28
nrepina
closed
1 year ago
0
Remove ovr_channel parameter since it is the same as org_seg_channel param
#27
nrepina
closed
1 year ago
0
Clean up logging for missing segmentations during feature extraction
#26
nrepina
closed
1 year ago
1
Separate organoid feature extraction into C01 (shape) vs. other ch features
#25
nrepina
closed
1 year ago
0
Add disconnected component detection for both 2D and 3D images (during featx)
#24
nrepina
closed
1 year ago
0
Maurice wish list of features
#23
nrepina
opened
1 year ago
0
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