dschneiderch / WalzPSIIProcessing

A pipeline to process multiframe tifs exported from ImagingWin .pim files

WalzPSIIProcessing

A pipeline to process multiframe tifs exported from ImagingWin .pim files

You will need to export your .pim files to multiframe .tifs and then drop them in data/raw_multiframe

They should be labeled with exactly 2 dashes, 2 descriptors, and a date: e.g. drought-20190501-sample1.tif

It is assumed the first descriptor is the treatment, the second descriptor is a sample number.

Additionally you will need pimframes_map.csv to describe each frame and genotype_map.csv to describe the genotype of each plant. It is important that metadata of your filename descriptors and your images match.

The contents of data/genotype_map.csv should have 3 column headers EXACTLY as specified here:

treatment, sampleid, roi, gtype
drought, sample1, 0, WT
drought, sample1, 1, m1
drought, sample1, 2, m1
drought, sample1, 3, WT

The contents of data/pimframes.csv should have 3 column headers EXACTLY as specified here:

imageid,frame,parameter
1,Fo,FvFm
2,Fm,FvFm
3,AbsR,AbsR
4,AbsN,AbsN
5,Fp,FvFm
6,Fmp,FvFm
7,Fp,t40
8,Fmp,t40

See example_data/ for complete examples and guidance.

To run the pipeline, make sure your plantcv python environment is in your path, then:

cd <project directory>
ipython scripts/psII.py

To change threshold values and the plant mask, modify psIImask() in src/segmentation/create_masks.py

At the very least, you will need need to modify scripts/psII.py in 2 places:

1. you must change indir to point to your data directory.
2. you must change the location of your roi's, currently on line 96 of scripts/psII.py. See plantcv documentation for details.