https://github.com/alleninstitute/cell_locator_tools
Tools for manipulating Cell Locator json files
Science Score: 13.0%
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Low similarity (7.5%) to scientific vocabulary
Repository
Tools for manipulating Cell Locator json files
Basic Info
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Metadata Files
README.md
Cell Locator json file converters
Render annotations in legacy json file(s) to an image volume
Directory VisualizationDraft contains Python scripts to convert Cell Locator json file(s) to a ITK compatible volume mask (eg nrrd, nii.gz)
python convertjson.py --jsonname input.json --outname output.nii.gz --atlasname averagetemplate10.nrrd
If parameter json_name is a directory, the output volume will contain the annotations of all json files in the directory each specified with a unique value. Scripts assumes non-overlapping annotations. Areas of overlapped are assigned to only one annotation with no guaranteed ordering.
This conversion code is known to work for annotations on the Allen Mouse CCF and Cell Locator outputs from version 0.1.0-2020-07-30.
The json file format changed after the Release 0.1.0-2020-07-30.
For newer format files, you can convert to legacy format before using rendering script.
Convert new format to legacy format json files
Directory ConvertBetweenJsonVersions contains Python scripts to convert newer format Cell Locator json files to legacy format.
python convertnewtooldjson.py --jsonname input.json --outname output_directory
Each annotation within the input.json is converted to individual json files in the output_directory. The output directory can be used as input for rendering script.
This conversion code is known to work for annotations on the Allen Mouse CCF and Cell Locator outputs from version 0.1.0-2020-09-18.
Convert legacy format to new format json files
Directory ConvertBetweenJsonVersions contains Python scripts to convert legacy format Cell Locator json files to new format.
python convertoldtonewjson.py --jsonname input.json --outname output.json
If parameter json_name is a directory, the output json will contain the annotations of all json files in the directory each specified by its filename (without extension) in the output.json file.
This conversion code is known to work for annotations on the Allen Mouse CCF and Cell Locator outputs from version 0.1.0-2020-07-30.
Level of Support
We are not currently supporting this code, but simply releasing it to the community AS IS. We are not able to provide any guarantees of support. The community is welcome to submit issues, but you should not expect an active response.
Copyright 2021 Allen Institute
Owner
- Name: Allen Institute
- Login: AllenInstitute
- Kind: organization
- Location: Seattle, WA
- Website: https://alleninstitute.org
- Repositories: 184
- Profile: https://github.com/AllenInstitute
Please visit http://alleninstitute.github.io/ for more information.
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