I am struggling to measure spheroid size in my microfluidic device. When I try to threshold the image, the outer microwell boundary is also getting included in the same. Because of which, I am not able to measure the area of only the spheroids. It is a big problem in cases where spheroid is touching the boundary of microwell. Becasue in that case I am not able to crop the image and exclude the wall areas. Any help would be appreciated.upper left.TIF (3.4 MB) thresholding.tif (3.0 MB)
Weka segmentation might be a decent option for this if your image acquisition is consistent over several images. Here’s a quick attempt (before and after segmentation).
More examples and more careful selection of the features of interest will of course provide better results. Weka segmentation can be found in FIJI > Plugins > Segmentation > Trainable Weka Segmentation.
@pedrolmoura Thank you so much for your input. I will try using this plugin.