MoMA tutorial introduction - nimwegenLab/moma GitHub Wiki

Table of contents

Introduction

This tutorial explains how to use MoMA to track cells in a growth lane. It is divided into two 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 lane with MoMA and perform manual curation.

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. 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).