Folders and files
| Name | Name | Last commit date | ||
|---|---|---|---|---|
Repository files navigation
Name: cyfi.py This program accepts the typical flow cytometry data in FCS2 (and maybe other formats) and interactively displays the 1D histogram or 2D scatter plots in a browser. Importantly, the program allows users to interactively define gates using the forward and side scatter plot. The selection is used to filter the events and generate a histogram of selected cells/beads. The interactive feature is implemented using the mpld3 library. The script has been validated using Anaconda-2.2.0 running python 2.7. It generates errors in Anaconda2-2.5 and does not run on Anaconda3 (which uses python 3.5). To run the program: 1. Start MongoDB. 2. python cyfi.py 3. Open 127.0.0.1:5000 in a browser The versions of various modules installed on my computer at the current time (and therefore compatible with this program) are listed in cyfi_requirements.txt.