## Table of contents

- [Introduction](#introduction)
- [Prerequisites](#prerequisites)

## Introduction

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

1. [Preprocessing](MoMA-tutorial-preprocessing): This part explains how to preprocess the data before analyzing it with MoMA.
2. [Processing in MoMA](MoMA-tutorial-tracking): 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](MoMA-Properties)).
- You have a dataset that you want to process. An example dataset is located [here](https://github.com/nimwegenLab/moma/wiki/moma-datasets).

### 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).