README.md

Gene expression data in AtlasViewer format

Each folder contains gene expression data in AtlasViewer format for a specific layer (L1, L2, L1&L2) and all cells.

To visualise patterns, first run AtlasViewer via atlasviewer/launch_aviewer.py. Drag and drop the segmentation file and the visualization widget and then drag and drop the pattern file. Select the genes to visualize form the right pane and click "Atlas gene expression" button from the AtlasViewer menu.

To read the .pat files in the folders:

import cPickle

fobj = file("patternFileName.pat")

patterns = cPickle.load(fobj)

fobj.close()

#patterns is a Python dictionary whose keys are genes and values are cell labels expressing the gene.