Live Cell Analysis - StarDist Segmentation

Fiji/ImageJ macro for analysis of live cell imaging data of mouse B cells.

Macro was developed by Cameron J Nowell of Monash University (cameron.nowell@monash.edu) in collaboration with Ben Croker (bcroker@ucsd.edu).

Code is based off of code published in Speir et al, Nat Immunol 2020 (doi: 10.1038/s41590-019-0550-7). Traditional watershed segmentation has been replaced with StarDist DeepLearning AI segemtnation from Schmidt et al, arXiv 2018 (doi: 10.1007/978-3-030-00934-2_30)

Code will take raw images in individual time point folders and combine them into hyperstacks for analysis. Analysis will count each cell type (CellTracker, PI and AnnexinV) and determine the percentage ammount of each. Percentages of double and triple positive populations are also determined. The analysis is designed so that any given cell is only ever counted and classified once.