Pre processing

Input data

We expect you have image data acquired with your Mother Machine. If a single time point looks anything like the sample image below, we are in business.

If you use fluorescence imaging, read our notes on Preprocessing Fluorescence Images.

Procedure

For a given image sequence, each growth channel is analyzed independently. For that matter we need to

1. align ("register") all frames of your image sequence
2. extract each growth channel as an independent dataset that can be processed by MoMA

The output of the pre-processing will be a sequence of image stacks, each containing all available time points and color channels for one of the growth channels.

Command line preprocessing

If needed, the preprocessing steps may be run from the command line.