mitosisanalyzer

Installation

Local workstation

Install Anaconda or Miniconda distribution on your computer. In a command line shell (e.g. Anaconda Prompt), execute the following commands:

git clone https://github.com/uvarc/mitosisanalyzer.git
cd mitosisanalyzer
conda env create -f environment.yml

Afton/Rivanna

In a Open OnDemand command line shell (Clusters > _HPC Shell), execute the following commands:

cd /standard/redemann_lab/apps
git clone https://github.com/uvarc/mitosisanalyzer.git
cd mitosisanalyzer
module load miniforge
mamba env create -f environment.yml

Running the MitosisAnalyzer application

Local workstation

In a command line shell, run the following commands:

conda activate mitoanalyzer
python mitoanalysis.py -i imagestack.nd2 -o my_outputdir -s 1 -d 2 -r 1

Afton/Rivanna (interactive)

Start an interactive Desktop session on Open OnDemand. Right clock on desktop to start a terminal session. In the terminal shell, run the following commands:

module load miniforge
source activate activate mitoanalyzer
cd /standard/redemann_lab/apps/mitosisanalyzer
python mitoanalysis.py -i imagestack.nd2 -o my_outputdir -s 1 -d 2 -r 1

Command line arguments**

-h, --help                             show 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
-p PROCESSES, --processes PROCESSES    optional: number or parallel processes
-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
-f FRAMERATE, --framerate FRAMERATE    optional: number of frames per second
-t THRESHOLD, --threshold THRESHOLD    optional: threshold of cytoplasmic background signal in spindle channel; value relative to max spindle intensity 0.0-1.0 (0.0=autodetect using
                    Otsu)