Flow Cytometry Tools

Flow Cytometry Tools

Flow Cytometry Tools

Overview

To help with the operation of the flow cytometry facility we have written a range of Python scripts to automate common tasks. We are putting these tools onto GitHub to help the flow cytometry community.
This program applies predefined sort templates to your BD Influx workspace. It can also take designs from Excel and apply them to your sort.
Autonomously monitor user sample quality for flow cytometers.  The idea is to test user sample quality by checking time vs fluorescence, as we do during analysis, but at the time of acquisition. This allows the core facility to be proactive helping our users spot problematic experiments and allows us to check for machine issues, such as recurrent blockages.
XDP sort stats
The BD Influx has a very useful feature that automatically saves sort statistics for every run. The XDP does not and if a user forgets, loses a print out or we accidently clear the stats (especially the total events) all the sort data is lost. However the XDP does save this information on the server! This script will extract this data and present it as a text file containing the sort statistics for each run on a given day.
This is a very simple script. It takes the bookings as inputted into the csv file and books them in PPMS.
Python script to email the last user of the day if they are operating outside office hours using data from PPMS
Influx Index exporter
BD Sortware for the Influx stores all the index data inside the .fcs file, however the common analysis tools (FlowJo, R etc.) cannot read this information. This script will export the index information and save it as .csv files.
INFLUX workspace renamer
BD Sortware for the Influx names all its files with non-descriptive names, however it can read any name a file has. When backing up and cleaning our PC we run this script to rename the workspace.xml files to the descriptive name as seen in Sortware itself.
INFLUX index file counter
When asked by management for statistics on index sorting by our customers we wrote this script. It will trawl though the folders and count the number of index .fcs files and the number of folders that contain them. We use a folder structure that allows us to count index experiments and users. It is: C:\INFLUX files\User 1\01Jan17\*.fcs
PPMS to HTML
We have a daily schedule TV in the lab and have produced a script to run this. The script queries the PPMS calendar system and produces a sorted HTML file of the day’s schedule.

Download and Installation

The tools can be found on Github at https://github.com/hally166

Authors

Sanger Contributors