Authors: Scott Brooks and Sara Toral Perez

git clone https://github.com/scottbrooks98/RLDecon

cd <repo>

conda env create -f environment.yml

Open anaconda prompt

conda activate flowdecimport

python C:\Users\u1604360\Documents\GitHub\RLDecon\RLDecon.py

• It should take in imageJ tifs not ome.tiffs - DONE
• It should take in 2 channel images and produce a deconvolution as a single tif - DONE
• Add a file chooser - DONE
• Step size entry, with default and reference to mdata DONE
• change the padding method (currently padded with 0s)
• change the number of iterations DONE

• Choose between Jonathan vs Scott fitting vs raw PSF
• threading
• output at every 5 iterations
• output ome.tiff as well

• Raw PSF Averaging
• sigma averaging

to get new z spacing after deskewing on warwick llsm, spacing*cos(57.2)

To run currently boot up flowdec anaconda