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threshold-based segmentation, coiled for N4/thresholding, BIDS app CLI, gubra and marmoset template, #18

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threshold-based segmentation, coiled for N4/thresholding, BIDS app CLI, gubra and marmoset template, #18

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@akhanf akhanf commented Nov 21, 2024 •
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This working branch has a lot of new features and fixes

major updates:

  • threshold-based segmentation workflow
    • performs field fraction quantifacation using otsu thresholding on N4 corrected data
  • use of coiled for dask rules
    • applying N4 and performing thresholding now done with coiled
    • TODO in future PR: make coiled optional
  • configured the BIDS app CLI (for spimquant console script), so we can use this instead of updating the config
    • TODO in future PR: add more CLI options for setting things like level, stain etc..
  • adds marmoset template (MBMv3)

To do before merging:

  • finish adding in Gubra template (was too large, need to incorporate downloading from zenodo into the workflow)
  • make a PR for snakebids (to use pybids 0.18.0, and the relative path fix)
  • make a release for latest zarrnii changes and point to that
  • maybe do the optional TODO's mentioned in the features above

akhanf added 30 commits October 13, 2024 23:46
@akhanf
reading from cloud storage
397c25a 
involves minor fixes to snakebids and pybids
@akhanf
fixes
641f727
@akhanf
updates to get deform_to_template working
c693e95
@akhanf
update cvpl-tools
9b6336e
@akhanf
update deps
38a6488
@akhanf
fix workflow bug
fdf75ad 
was not using stain_for_reg for penalty mask
@akhanf
remove print
49d1b27
@akhanf
add wip MIP example with coiled
751178d
@akhanf
add WIP sandbox notebook on various analyses
9bb6e98
@akhanf
some more updates -- couldn't get upsampling to work!
3789f01
@akhanf
updtes to get n4 a p plied by seb
e917f05
@akhanf
nearly completed workflow with n4, threshold, density
3d76a74
@akhanf
recent changes
0b72cd0
@akhanf
add antspyx dependency
ae7f537
@akhanf
WIP - adding n4 and coiled otsu to workflow
15f992f
@akhanf
working up to otsu mask
2820cc5
@akhanf
use updated ZarrNii downsampling upon construction
6c9939f 
- now we don't need to downsample z and determine what downsampling
rates to use
- this is done internally in ZarrNii depending on the specification of
the level

- also added rules for getting fieldfrac roi atlas space images
@akhanf
updates before rerunning on all up to n4
b298735
@akhanf
fix to get fieldfrac working, uses updated zarrnii
0638e93
@akhanf
updated params, use coiled resource
cf63339 
also started updating cli
@akhanf
remove extra
73bb440
@akhanf
updates for oldBlaze
74467ea
@akhanf
fix typo, extend idle timeout
064c126
@akhanf
WIP analysis script
c6d1705
@akhanf
wip analysis notebook, add template-warped outputs
57c5bc7 
also change idle_timeout
@akhanf
add default profile for rerun triggers
adaa1b7
@akhanf
add PI deformed
03d73d5
@akhanf
don't add group neg mask yet
ceab3ab
@akhanf
add group avg
dbf9b83
@akhanf
create negative mask from group subset and apply
6a08e41
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@akhanf