Quick user guide

This quick user guide gives a short guide through how to run the MoMA Fiji plugins in order to process your data.

1. Input data organisation

Assuming you used your Microscope to acquire a series of images showing the mother machine as a time series. Every image should only contain a single 2D image. Thus, if you acquired two colour channels, there should be two image files per time frame. The files should all be located in one folder. Filenames should contain the sequence _tx_ty.tif, where x corresponds to the time frame number and y corresponds to the channel number. Both x and y must include leading zeros so that the numbers always have 4 digits. An example folder may look like that:


The images should furthermore look like this: 

1. Mother Machine Analysis

Run MoMA from the Fiji menu entry Plugins > MoMA > MoMA pipeline. A dialog will open. Enter the folder location where the images are saved and furthermore the number of acquired color channels:


MoMA will now preprocess the images. This means image registration between time frames and extracting growth channels which will be listed and further processed afterwards. If there are any issues with these steps, look here for detailed information on:

• [Image](Image Registration) and
• [Growth](Growth Channel Separation)

After the growth channels were separated, Fiji will automatically open a dialog where you can select the growth channel dataset to work with:


MoMA will then open and allow you to work with the data set:


Details on the main user interface can be found here:

• [MoMA:](MoMA#the-moma-user-interface)

Use the _Export data_ button to finally save your analysis results. A dialog will show up, where you can select what to export.


When saving, you can change the output folder manually. It is recommmend to not do this, because if you keep the suggested output folder, MoMA can differentiate between growth channels which were processed already and which not. Thus, when you run the _MoMA pipeline_ plugin again, you will see a * marker behind all data sets which were analysed already.

1. Output data organisation

MoMA generates inside the input folder a new folder structure representing the individual processing steps. The analysis result data is stored in the folder _3 analysed_ :


Further information on the structure of the analysis files can be found here:

• [Post-processing](Post-processing)