MoMA tutorial introduction - nimwegenLab/moma GitHub Wiki

This tutorial explains how to use MoMA to track cells in a growth lane. It is divided into three parts:

  1. Preprocessing: This part explains how to preprocess the data before analyzing it with MoMA.
  2. Processing in MoMA: This part explains how to track cells in a growth channel with MoMA and perform manual curation.
  3. Batch processing: This part explains how to analyse many growth channels in batches.

Prerequisites

This tutorial assumes:

  • You have correctly setup and configured MoMA and a correctly configured mm.properties file in your home directory (see here).
  • You have a dataset that you want to process, acquired with Micro-Manager. An example dataset is located here.

Paths used in this tutorial

It also uses the following space-holder variables that you will have to replace with the correct paths.

[!WARNING] The space-holder variables are also used in the example-scripts, commands and code-snippets in this tutorial. You will have to replace them there as well.

  • <PATH_TO_FIRST_OME_TIF_MEASUREMENT_FILE>: Path to the first OME-TIFF file of the dataset that you want to process. It will be something like /path/to/my/dataset/dataset.ome.tif, where the folder /path/to/my/dataset/ may contain additional files of the OME-TIFF stack, e.g.: dataset_1.ome.tif, dataset_2.ome.tif, etc.
  • <PATH_TO_FIRST_OME_TIF_FLATFIELD_FILE>: Path to the first OME-TIFF file of the flatfield images that correspond to the dataset that you want to process. It will be something like /path/to/my/flatfield/flatfield.ome.tif, where the folder /path/to/my/flatfield/ may contain additional files of the OME-TIFF stack, e.g.: flatfield_1.ome.tif, flatfield_2.ome.tif, etc.
  • <ANALYSIS_DIRECTORY>: Folder-path where the analysis results will be stored. It will contain the preprocessed-data, the template for splitting growthlanes and the final tracking results (this will become apparent during the tutorial).

Semantics

We refer to the microfluidic channels in which bacteria grow in line as "growth lane" (GL) or "growth channel" (GC).