Quick user guide
This quick user guide gives short instructions on how to run the MoMA Fiji plugins in order to process your data.
We assume your microscope acquired a series of images showing the mother machine as a time series, e.g. looking like this:
If you use fluorescence imaging, read our notes on Preprocessing Fluorescence Images.
Either the images are saved as image stack in .tif format. If not, MoMA expects a folder of 2D images, one image file per time frame. If you acquired two colour channels, there should be two image files per time point. The files should all be located in one folder. Filenames should contain the sequence _tx_cy.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 would look like this:
After starting Fiji, run MoMA from the Fiji menu entry Plugins > MoMA > MoMA Application processing a file or folder. A dialog will open asking for the file/folder location where the raw image sequences are saved:
After clicking Ok, MoMA will preprocess the images. The first step is image registration between time frames. The second step is extracting growth channels which will be listed and further processed afterwards. Both processes are fully automatic. If there are any issues with these steps, look here for detailed information:
After the growth channels are separated, MoMA will open a dialog where you can select the growth channel dataset to analyse:
MoMA will then open the main user interface allowing curation of an automatically determined tracking solution:
Click the "Optimise" button in order to display a first potential tracking solution. Details on the main user interface can be found here:
Use the Export data button to finally save your analysis results. A dialog will show up, where you can select what to export:
When exporting data, you can change the output folder manually. It is recommmend to keep the suggested output folder, because then 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.
MoMA generates new subfolders inside the input folder representing the individual processing steps. The analysis result data is stored in the folder 3 analysed :
Further information on the structure of the analysis result files can be found here: