Blobdetect lc #15
Blobdetect lc #15
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Karl5766
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| """ | ||
| input: | ||
| zarr='/path_to_bids_root/bids/sub-onuska21/micr/sub-onuska21_sample_brain_acq-prestitched_SPIM.ome.zarr?slices=[1]', | ||
| neg_mask='/path_to_bids_root/resources/onuska21_patched.tiff', |
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I know still a work-in-progress, but we should use a different format for the neg_mask -- either ome.zarr or nifti (and use zarrnii to get in the same space)
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Thanks for the pointer! I was wondering which format would work better in this case
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Is there a rescaling component on the original OME ZARR image? Or only neg_mask is scaled but the OME ZARR is kept as scale=diag(1, 1, 1, 1)
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Is there a rescaling component on the original OME ZARR image? Or only neg_mask is scaled but the OME ZARR is kept as scale=diag(1, 1, 1, 1)
You're asking about how to go from voxel to physical coordinates? The vox2ras matrix from zarrnii does that for you. Perhaps can go over on a call or when I'm back on Friday.
| spimquant bids_dir output_dir {participant} [snakemake_args] | ||
| # now since we run spimquant, contents in config/snakebids.yml has changed | ||
| # and we can run snakemake with the updated configuration | ||
| snakemake result_file_path |
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not sure why you need this -- the spimquant cli runs snakemake already --
| A more concrete example: | ||
| ```bash | ||
| spimquant test_bids_dir test_out participant | ||
| snakemake results/result_image.nii -n |
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You can specify targets using the spimquant cli too.. e.g. spimquant test_bids_dir test_out participant -n results/result_image.nii
So there isn't a need to instruct the user to run snakemake directly..
Integrating the masked global labeling pipeline into SPIMquant.
(This PR is based on the other PR that hasn't been merged)
A bit unsure what parameters to define for the rule
negatively_masked_countinginblobdetect.smk: The mask file is a tiff that may need to be rescaled to fit the size of the image. Thetmp_pathis a place for storing cached files but in the snakebids file I'm not sure if any folder specified there is used for temporary files.Probably will make some changes later depending on what need to be done in order for this PR to be suitable for merge.