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scripts
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README.md
methodology.md
requirements.txt

README.md

README

Scripts to identify plasmodesmata in cells.

For information about the algorithm see the methodology.

Installation notes

Dependencies

Notes on how to install bftools and FreeImage can be found in the jicbioimage installation notes

Windows

Install the Anaconda Python distribution.

Setup a virtual environment named find_plasmodesmata_env and install the scientific Python package dependencies.

conda create –n find_plasmodesmata_env python=2.7 numpy scipy scikit-image

Activate the virtual environment.

activate find_plasmodesmata_env

Install the jicbioimage dependencies.

pip install jicbioimage.transform

Download the find_plasmodesmata project from githq and go into it.

Linux

Clone the project from githq and go into it.

git clone git@github.com:JIC-CSB/find-plasmodesmata.git
cd find-plasmodesmata

Install the dependencies.

pip install numpy
pip install scipy
pip install scikit-image
pip install jicbioimage.transform

Data analysis

On Windows remember to activate the virtual environment when you open a new command prompt.

activate find_plasmodesmata_env

To run the analysis on a specific series in an input microscopy file one can use the scripts/plasmodesmata_anlaysis.py script. The command below analyses the first series in the file (zero-indexed).

python scripts/plasmodesmata_analysis.py /path/to/raw/file/of/interest.lif 0 output_directory

To run the analysis on all series in an input microscopy file run the command below.

python scripts/analyse_all_series.py /path/to/raw/file/of/interest.lif output_directory

To run the analysis on lots of microscopy files in a directory one can use the scripts/analyse_all_images.py script.

python scripts/analyse_all_images.py /path/to/input_dir output_directory