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.
You can install mitosisanalyzer via pip:
pip install mitosisanalyzer
To install latest development version :
pip install git+https://github.com/uvarc/mitosisanalyzer.git
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
Contributions are very welcome.
Distributed under the terms of the BSD-3 license, "mitosisanalyzer" is free and open source software
If you encounter any problems, please file an issue along with a detailed description.