gitignore and obsolete files

.gitignore

 *~
+*.lsm
+*.h5
+*.hdf
 *.asv
 *.mat
-.Rhistory
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+.Rhistory

README.md

+# NPC maturation
+This repositories contains code and data for the anlysis and computational modelling of NPC maturation
+
+## Extract cytoplasmic and nucleoplasmic intensities in the absence of an external marker
+This pipeline combines ilastik, and matlab workflows. Images are typically starting from metaphase.
+1. Convert lsm files to hdf5 for reading in ilastik
+2. For a given cell line create or reuse a classifier (ilastik 1.8)
+3. Process all files and save segmented images
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