How to launch batch processing

[Estelle B]

Hi all,

I am new to MicrobeJ (using 5.13o (17)) and would like to batch process my images. I can't find any help/tutorial on the MicrobeJ website.

I have all the settings working to analyse my images.

I am not sure what to do once the batch window is opened. If I load images, they are not recognised as separate channels. If I load nd2 files, the mask image is not included.

What should I do?

Thanks for your help!