Cell segmentation with Find Maxima

I have trouble with the ‘Find maxima – output segmented particles’ in FIJI.

‘Find maxima’ works to output from the original image: point selection, single points, counts, etc… but when I select the option for ‘segment particles’, it does not result in an image with delineated particles.

Does anyone else encounter this error? How can I resolve this?

Typical image is 16-bit, single channel TIF example image

Load image
Find maxima (noise tolerance=100, output=segment particle)

Once it starts, it stays at 5% and does not progress.


What exactly is the trouble? With the output of ‘Segmented Particles’ selected… you should get the image of the delineated particles. But running it again - on the original image - with an output of ‘Point Selection’… you should get the ROIs you need (as multi-point selections) and save them to the ROI Manager if desired.

Perhaps it’s worth re-visiting the associated section in the ImageJ User Guide regarding outputs from this tool?

Otherwise… describe again in detail the exact steps you are doing and where things go ‘wrong’ for you and how. Sharing an original image that you are using is also helpful - you can share it directly here on this thread or via a link to a file-sharing site.