Preprocessing Fluorescence Images

This page describes how to analyze fluorescence image data in MoMA. If your data looks anything like this image, please read the following instructions.

In general the quick user guide is also applicable for fluorescence imaging. The additional steps listed below only apply to preprocessing, running MoMA should work the same way it does for phase contrast image data.

You can also try this using our example data.

Preparing the dataset

• The first channel of the input file(s) has to contain the fluorescence image data. If your input data contains more channels and the fluorescence image is not placed first, please adjust the data. In Fiji this can be done using Image → Stacks → Tools → Stack Splitter
• In contrast to preprocessing phase contrast images, the image data has to be aligned straight (vertical growth lines). Slightly rotated input data will not be aligned during preprocessing and will therefore produce false results. You can rotate the data in Fiji using Image → Transform → Rotate...

Preprocessing

During growth channel separation two additional options are relevant.

• Check No phase contrast
• Add the estimated width of the growth line to Fake GL width (in pixel). To measure the width with Fiji use the line tool to draw a line horizontally through the growth line. Go to Analyze → Set Scale and copy the value shown in Distance in pixels

Issues

Please contact us if you are not able to analyze your fluorescence image data using MoMA.