sarahmulloy/Fluorescent-image-automatic-object-detection: Python and cellprofiler Automatic object detection in fluroescent images

This analysis pipeline has been used to quantify fluorescent probe expression in multiplex RNAscope, immunohistochemistry, and viral fluorescent targeting in neuroscience histology work. This repository includes a python script to crop ROI images across fluorescent channels, cell profiler software to identify fluorescent probe location within defined cell regions, and post-analyze the probe-positivity and co-expression in each cell using robust threshold methods. The result is quantified cell positivity expression and amount of fluorescent puncta ('occupancy') expressed in each cell for 3 fluorescent channels. Code is adapted from original matlab script developed by Runbo Gao (Gao et al. 2024) in Dr. Anna Lee's research lab at the University of Minnesota. Gao R, Schneider AM, Mulloy SM, Lee AM. Expression pattern of nicotinic acetylcholine receptor subunit transcripts in neurons and astrocytes in the ventral tegmental area and locus coeruleus. Eur J Neurosci. 2024 May;59(9):2225-2239. doi: 10.1111/ejn.16109. Epub 2023 Aug 4. PMID: 37539749; PMCID: PMC10838369.