Tracking with pre-specified overlay

[Theorell]

Hi,
I have an image sequence with a pre-specified cell segmentation in the form of an image overlay (.tif), for which I want to perform frame-to-frame tracking in microbeJ. As I understand from the documentation, I have to do this using a binary-mask. How should I turn my (existing) image overlay into a binary mask that is recognized by microbeJ?

[MicrobeJ]

Hi,

Yes, MJ works with user-defined binary-masks or uses auto-thresholding or local maxima detection methods to detect particles.

Do you have an example of your image overlay? It might help to figure out the best way to convert the overlay image into something intelligible for MJ.

Let me know,

Adrien

[Charlotte Bost]

Hi,

I am also trying to use a binary mask to outline the cells instead of using thresholding. However, I don't understand how to proceed. In the window "images" I selected the 'binary mask' but none of my opened images seem to be recognized as masks. Even when I do have a binary image open in Fij, the only option that I can choose as a mask is 'none'. Is it a problem of my mask not being recognized by microbeJ ? 

I have the version 5.13l - October 8, 2020 of microbeJ. Joined as attachment is an example of a mask. 

Best,

ps: I am using microbeJ for mitochondria detection but still quite good^^