mitosisanalyzer

Plugin to track spindle poles in mitotic cells over time. It leverages Cellpose, OpenCV, and Scikit-Image for segmentation and Prefect and Dask for workflow orchestration.

Installation

You can install mitosisanalyzer via pip:

pip install mitosisanalyzer

To install latest development version :

pip install git+https://github.com/uvarc/mitosisanalyzer.git

Running the MitosisAnalyzer application

In a command line shell, run the following command:

mitosisanalyzer -i imagestack.nd2 -o my_outputdir -s 1 -d 2 -r 1

Command line arguments:

    -h, --help                                show this help message and exit
    -i INPUT, --input INPUT                   .nd2 file or directory with .nd2 files to be processed
    -o OUTPUT, --output OUTPUT                output file or directory
    -s SPINDLE, --spindle SPINDLE             channel # for tracking spindle poles
    -d DNA, --dna DNA                         channel # for tracking dna
    -r REFFRAME, --refframe REFFRAME          reference frame to determine spindle pole axis (0=autodetect based on cell long axis)
    -t THRESHOLD, --threshold THRESHOLD       threshold of cytoplasmic background signal in spindle channel; value relative to max 
                                              spindle intensity 0.0-1.0 (0.0=autodetect using Otsu)
    -b BLUR, --blur BLUR                      applies a gaussian blur before segmenting spindle poles. The value determines the 
                                              blurring radius; a value of 0 omits blurring.
    -c, --cellpose, --no-cellpose             use Cellpose to detect cell contour
    -f FRAMERATE, --framerate FRAMERATE       number of frames per second
    -e EXECUTOR, --executor EXECUTOR          set executor. Options: sequential, concurrent, dask
    -p PROCESSES, --processes PROCESSES       number or parallel processes

Contributing

Contributions are very welcome.

License

Distributed under the terms of the BSD-3 license, "mitosisanalyzer" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.