https://github.com/alleninstitute/patchseq_autotrace
Execution of patchseq slice autotrace pipeline
Science Score: 26.0%
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○Scientific vocabulary similarity
Low similarity (13.3%) to scientific vocabulary
Repository
Execution of patchseq slice autotrace pipeline
Basic Info
- Host: GitHub
- Owner: AllenInstitute
- Language: Python
- Default Branch: master
- Size: 22 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
patchseq-autotrace
This package supports the patchseq autotrace pipeline to generate automated neuron morphological reconstructions.
Installation instructions
conda create -n autotrace_env python=3.9
conda activate autotrace_env
git clone https://github.com/AllenInstitute/patchseq_autotrace.git
cd patchseq_autotrace
pip install -r requirements.txt
pip install .
Internal Allen Institute Use
In order to download image stacks from the internal LIMS system, you must set certain OS environment variables to connect properly. These include
LIMS_HOST
LIMS_DBNAME
LIMS_USER
LIMS_PASSWORD
To set these either open a terminal and run the following commands or add the commands to your .bashrc file.
export LIMS_HOST=yourdbhostname
Contact the technology team if you need to get credential details to access LIMS.
Scripts
After installation the following console scripts will be available to run from the command line of your environment. To see detailed instructions on each script type the name of the SCRIPT_NAME --help
auto-patchseq-pipeline-hpc
script to submit a batch of cells to run on the allen hpc. Creates a DAG workflow composed of the following scripts
auto-pre-proc
script to prepare an already existing image stack, or obtain from LIMS and prepare an image stack for segmentation
auto-segmentation
script to segment the resulting images from auto-pre-proc
auto-post-proc
script to post-process and skeletonize the segmented image stack generated by auto-segmentation
auto-skeleton-to-swc
script to convert the skeletonized image generated in auto-post-proc to an swc file
auto-cleanup
script is run at the end of the pipeline (after auto-skeleton-to-swc), or if any of the intermediate steps fail to remove large files from disk.
Statement of Support
This code is an important part of the internal Allen Institute code base and we are actively using and maintaining it. Issues are encouraged, but because this tool is so central to our mission pull requests might not be accepted if they conflict with our existing plans.
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.
GitHub Events
Total
- Push event: 13
- Pull request event: 2
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Last Year
- Push event: 13
- Pull request event: 2
- Create event: 2
Issues and Pull Requests
Last synced: 11 months ago
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- Total pull requests: 7
- Average time to close issues: N/A
- Average time to close pull requests: 2 minutes
- Total issue authors: 0
- Total pull request authors: 2
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 7
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: less than a minute
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
Pull Request Authors
- MatthewMallory (8)
- sarahwallingbell (1)