wbonelli/vessel-detector repository overview

⁠Vessel Detector

Detects injection-filled and empty vessels in stem tissues.

Author: Suxing Liu (adapted by Wes Bonelli)

⁠Requirements & Installation

The easiest way to run this project in a Unix environment is with Docker⁠ or Singularity ⁠.

⁠Usage

To explore the vessel-detector image, open a shell inside it:

docker run -it -v "$(pwd)":/opt/vessel-detector -w /opt/vessel-detector wbonelli/vessel-detector bash

A good way to get started is to run the tests:

docker run -it -v "$(pwd)":/opt/dev -w /opt/dev wbonelli/vessel-detector python3 -m pytest -s

⁠Docker

To run with Docker, use a command like:

docker run -it -v "$(pwd)":/opt/vessel-detector -w /opt/vessel-detector wbonelli/vessel-detector python3 vd.py detect <input file> -o <output directory> -mr <minimum vessel radius> -ft <filetypes, comma-separated>

⁠Singularity

To use Singularity:

To use Singularity:

singularity exec docker://wbonelli/vessel-detector python3 vd.py detect <input file> -o <output directory> -mr <minimum vessel radius> -ft <filetypes, comma-separated>

⁠Supported filetypes

By default, JPG, PNG, and CZI files are supported. To limit the analysis to certain filetypes, use the -ft flag (a comma-separated for multiple), for instance: -ft png,czi.