This GitHub repository provides the scripts to processing and analysis scripts for OXT/cFOS/DAPI-stained immunofluorescent image stacks acquired from Zeis LSM700 confocal microscope. Data from this analysis is published by Maynard et al., in prep, insert link to publication.

• Project phenotype data is generated using the make_pheno.R script by parsing the precisely named file names.

• Primary processing and data extraction is done using a custom MATLAB script cellSegCFOS.m. This custom function was ran with MATLAB 2016b and requires the CellSegM Matlab toolbox (https://github.com/ehodneland/cellsegm).

• Batch execution and summarization of extracted data into the R environment requires running the R script preprocess_cFOS_v2.R on an SGE compute cluster. Processed data files can be requested from the authors.

Main statistical analysis for this dataset occurs in the Rscript analyze_cFos_v2.R.

• Nested image dataset (3 wild-type vs. 3 mutant animals, 6-9 image stacks per animal, N=48 total)
• Image are tile-stitched in x & y, retaining z information
• PVN area are image-dependent and must be computed to adjust for # of OXT (+) cells in view