ophys_nway_matching
N-way matching of segmented cell ROIs
Docker and Singularity
A docker image is built in CircleCI and pushed to dockerhub tagged as either master or develop.
Singularity should be able to run this docker image directly:
singularity run docker://alleninstitutepika/ophys_nway_matching:develop python -m pytest /ophys_nway_matching
or
singularity run docker://alleninstitutepika/ophys_nway_matching:develop python -m nway.nway_matching --help
It appears the calling singularity in this way intelligently uses the local caches for both docker and singularity. There is an overhead for downloading an updated docker image and translating it to a singularity image. That cost is incurred only when the docker image has changed.
quick start
conda create -n nwaytest python=3.6.4
conda activate nwaytest
pip install git+https://github.com/AllenInstitute/ophys_nway_matching
python -m nway.nway_matching --input_json tmp_example/input.json --output_json tmp_example/output.json
This creates tmp_example/output.json. The intent is that this file contains everything you need to know, both results and diagnostic metrics.
Some basic visualizations of the results are in nway.diagnostics
python -m nway.diagnostics --input_json tmp_example/output.json --output_pdf tmp_example/output.pdf
This should create tmp_example/output.pdf.
Level of support
We are not currently supporting this code, but simply releasing it to the community AS IS but are not able to provide any guarantees of support, as it is under active development. The community is welcome to submit issues, but you should not expect an active response.