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hubmapconsortium
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codex-pipeline
CODEX data processing code
GNU General Public License v3.0
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Remove references to defunct antibodies util
#57
pennycuda
closed
1 month ago
0
Bump black from 22.10.0 to 24.3.0
#56
dependabot[bot]
opened
5 months ago
0
Update Python dependencies
#55
pennycuda
closed
9 months ago
0
Update Python dependencies
#54
pennycuda
closed
9 months ago
0
Update dependencies
#53
pennycuda
closed
9 months ago
0
Standardize antibody names and add structured annotations
#52
pennycuda
closed
9 months ago
0
modified ometiff_second_stitching.cwl and run_cytokit.cwl in steps folder
#51
nikhilyerra
opened
9 months ago
0
Pennycuda/standardize antibody names squashed
#50
pennycuda
closed
9 months ago
1
Use channel names from `antibodies.tsv`
#49
pennycuda
closed
9 months ago
0
Pennycuda/standardize antibody names
#48
pennycuda
closed
10 months ago
0
create preprocessing module for 3D CODEX images
#47
rfmurphy
opened
10 months ago
0
test new version of deepcelltype
#46
rfmurphy
opened
10 months ago
0
Update/fork to handle PhenoCycler (+Fusion)
#45
mruffalo
opened
11 months ago
1
Marking pipeline outputs as data products
#44
SFD5311
closed
11 months ago
0
Translate imagecodecs exception to RuntimeError
#43
jswelling
closed
1 year ago
0
Welling/fix cwl parameter
#42
jswelling
closed
9 months ago
0
Update pipeline to work with modern dependencies
#41
mruffalo
opened
1 year ago
0
Pin Anaconda/Miniconda version to py39_4.12.0
#40
mruffalo
closed
1 year ago
0
Can't build images without Docker build cache
#39
mruffalo
closed
1 year ago
0
Control degree of parallelism from dask in run_background_subtraction
#38
jswelling
closed
1 year ago
1
Replace implementation of run_background_subtraction.assign_fraction_of_bg_mix
#37
jswelling
closed
1 year ago
1
make get_ch_stack_ids robust against missing names
#36
jswelling
closed
1 year ago
0
Changes to ometiff conversion to use stripped down antibody names and…
#35
SFD5311
closed
9 months ago
0
codex-pipeline with singularity
#34
asom
opened
1 year ago
0
Fix manifest(s) for split pipeline
#33
mruffalo
closed
1 year ago
1
Switch to DeepCell
#32
mruffalo
opened
2 years ago
0
Port BigTIFF usage from `czi-handling` branch for Vanderbilt datasets
#31
mruffalo
opened
2 years ago
0
Handle new meta
#30
VasylVaskivskyi
closed
2 years ago
0
Update for ImmunoSABER
#29
mruffalo
opened
2 years ago
0
Define and implement new CODEX data standard
#28
mruffalo
opened
2 years ago
0
Implement and use new CODEX metadata standard
#27
mruffalo
opened
2 years ago
0
tutorial to follow
#26
sailseem
opened
2 years ago
1
Read new metadata file `dataset.json`
#25
mruffalo
opened
2 years ago
0
Support "all" GPUs
#24
mruffalo
opened
3 years ago
0
Add pipeline option(s) to control CPU parallelization
#23
mruffalo
closed
1 year ago
1
Group CPU pipeline steps
#22
mruffalo
closed
3 years ago
2
Split CPU and GPU operations into top-level pipelines
#21
mruffalo
closed
3 years ago
2
Implement background correction
#20
mruffalo
closed
3 years ago
0
Implement cross-tile correction to avoid visible patterns in stitched data sets
#19
mruffalo
closed
3 years ago
1
Cell IDs improperly merged after stitching
#18
mruffalo
closed
3 years ago
1
Write some descriptive measures to a text or JSON file at end of pipeline
#17
mruffalo
closed
3 years ago
0
Incorporating stitching and other changes
#16
VasylVaskivskyi
closed
3 years ago
0
Add 'extras' directory to list of dir names excluded from raw data
#15
jswelling
closed
3 years ago
1
Add a LICENSE file
#14
ngehlenborg
closed
4 years ago
1
SPRM json addition
#13
tCeZ
closed
4 years ago
0
Prune outputs of pipeline
#12
mruffalo
closed
3 years ago
2
Handle channel names report CSV files
#11
mkeays
closed
4 years ago
1
Write physical dimensions in OME-TIFF output files
#10
mruffalo
closed
4 years ago
0
Add SPRM step
#9
mkeays
closed
4 years ago
0
Remove Nextflow support
#8
mkeays
closed
4 years ago
0
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