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https://github.com/alleninstitute/sptx_ccf_registration

Spatial Transcriptomics - CCF Registration

https://github.com/alleninstitute/sptx_ccf_registration

Science Score: 13.0%

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Repository

Spatial Transcriptomics - CCF Registration

Basic Info
  • Host: GitHub
  • Owner: AllenInstitute
  • License: other
  • Language: Python
  • Default Branch: main
  • Size: 9.2 MB
Statistics
  • Stars: 3
  • Watchers: 3
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created almost 3 years ago · Last pushed over 2 years ago
Metadata Files
Readme License

README.md

Spatial Transcriptomics to Common Coordinate Framework Registration

Overview

sptxccfregistration is an image processing pipeline for registering spatial transcriptomics data to the common coordinate framework (CCF). This pipeline consists of three modules:

  1. Segmentation of MERFISH point cloud data consisting of cell label and position into regions
  2. Registration of MERFISH labels to CCF labels
  3. Dashboard for analyzing the registration through metrics and image visualization

image

Installation

  1. Clone this repository: git clone https://github.com/AllenInstitute/sptx_ccf_registration
  2. Navigate to the directory: cd sptx_ccf_registration
  3. Install the package: pip install .
  4. Install dependencies for Neuroglancer pip install -r requirements_neuroglancer.txt
  5. For Neuroglancer, obtain AWS credentials and export to your environment

Usage

For detailed usage instructions, see the documentation for individual modules in docs

You can use the following commands to get help on the input params for each module: python -m sptx_ccf_registration.segmentation --help python -m sptx_ccf_registration.registration --help python -m sptx_ccf_registration.metrics_dashboard --help

You can configure these parameters with an inputjson file for each module. Examples of these can be found in the `sampleconfig` directory.

Here are examples of launching the modules with the inputjson files. ``` python -m sptxccfregistration.segmentation --inputjson sampleconfig/segmentation/segmentationbroad.json python -m sptxccfregistration.segmentation --inputjson sampleconfig/segmentation/segmentationlandmark.json python -m sptxccfregistration.registration --inputjson sampleconfig/registration/registration.json python -m sptxccfregistration.metricsdashboard --inputjson sampleconfig/metricsdashboard/metricsdashboard.json ```

Owner

  • Name: Allen Institute
  • Login: AllenInstitute
  • Kind: organization
  • Location: Seattle, WA

Please visit http://alleninstitute.github.io/ for more information.

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Dependencies

requirements.txt pypi
  • alphashape *
  • antspyx *
  • argschema *
  • numpy *
  • pandas *
  • rasterio *
requirements_neuroglancer.txt pypi
  • SimpleITK *
  • cloud-volume *
  • dask *
  • dominate *
  • h5py *
  • ome-zarr *
  • pandas *
  • s3 *
  • task-queue *
src/sptx_ccf_registration/metrics_dashboard/ccf_merfish_metrics/requirements.txt pypi
  • Flask *
  • beautifulsoup4 *
  • lxml *
  • markdown *
  • pandas *
  • plotly *
setup.py pypi