Scripts to identify plasmodesmata in cells.
For information about the algorithm see the methodology.
Notes on how to install bftools
and FreeImage
can be found in the
jicbioimage installation notes
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.
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
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