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khanlab
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SPIMprep
A Snakemake workflow for pre-processing single plane illumination microscopy (SPIM, aka lightsheet microscopy)
MIT License
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Update versions of dependencies
#41
akhanf
closed
1 week ago
0
Integrate QC report generation into the workflow
#40
BenGros
closed
1 week ago
4
update to accommodate differing numbers of stains/channels
#39
akhanf
closed
2 months ago
1
Dealing with samples with more or less than 2 channels/stains
#38
akhanf
closed
2 months ago
0
Create a small test dataset and add tests
#37
akhanf
opened
2 months ago
0
Add documentation with mkdocs
#36
akhanf
closed
2 months ago
0
Add option to write BIDS directly to cloud storage
#35
akhanf
closed
1 week ago
1
Add additional bids microscopy metadata
#34
akhanf
opened
3 months ago
0
Alternate workflow for data that is already stitched (prestitched)
#33
akhanf
closed
3 months ago
0
fix physical size bug in BIDS metadata
#32
akhanf
closed
3 months ago
0
incorrect voxel dimensions in derivatives/resampled
#31
akhanf
closed
3 months ago
2
samples.tsv can have duplicates if same samples with different acq flags
#30
akhanf
opened
3 months ago
0
set localrule for anything not in group preproc
#29
akhanf
closed
3 months ago
0
Report generation
#28
akhanf
opened
3 months ago
1
Documentation
#27
akhanf
opened
3 months ago
1
Clean-up SPIM JSON file
#26
akhanf
opened
3 months ago
0
run bids-validator as a final step
#25
akhanf
opened
3 months ago
0
BIDS top-level files and metadata updates
#24
akhanf
closed
3 months ago
0
python3.12 and invalid escape sequences
#23
akhanf
opened
3 months ago
0
fix to use work ome-zarr as input for nifti conversion
#22
akhanf
closed
3 months ago
0
bids dataset doesn't have a README
#21
akhanf
closed
3 months ago
0
samples.tsv is required for bids-compliance (and optionally samples.json)
#20
akhanf
closed
3 months ago
0
SPIM.metadata.json file not bids-compliant
#19
akhanf
closed
3 months ago
0
fix: was missing directory() in ome-zarr rule
#18
akhanf
closed
3 months ago
0
update workflows
#17
akhanf
closed
3 months ago
0
Zarr updates
#16
akhanf
closed
3 months ago
0
remove atlas registration rules
#15
akhanf
closed
3 months ago
0
renamed spim to SPIM (for BIDS compliance)
#14
akhanf
closed
3 months ago
0
Units incorrect (mm vs um)
#13
akhanf
closed
3 months ago
0
Change case of spim outputs
#12
akhanf
closed
3 months ago
0
Make zipped outputs optional (not the default)
#11
akhanf
closed
3 months ago
0
Consider what other minimal pre-processing steps should be included
#10
akhanf
opened
5 months ago
1
fix for tar inputs
#9
akhanf
closed
5 months ago
0
chore: release 1.0.0
#8
github-actions[bot]
closed
5 months ago
0
fix: actually fix the bug that disabled stitching
#7
akhanf
closed
5 months ago
0
feat: add support for writing omero metadata
#6
akhanf
closed
5 months ago
0
Make the intensity_rescaling on a per-channel basis
#5
akhanf
opened
5 months ago
0
Add omero metadata to the ome.zarr so channel names can be provided
#4
akhanf
closed
5 months ago
1
Fix: Dimension separator fix, other refactoring
#3
akhanf
closed
5 months ago
0
feat: made raw_tif_glob redundant for simplicity
#2
akhanf
closed
5 months ago
0
build: update actions to perform linting and minimal dry-run testing
#1
akhanf
closed
5 months ago
0