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ariel-waisman / LabelsToROIs

A Fiji/ImageJ plugin to generate ROIs from label images, allowing ROI erosion and quantification
GNU General Public License v3.0
21 stars 9 forks source link

exclude cells on edges #8

Closed JustineJiao closed 2 years ago

JustineJiao commented 2 years ago

Hi there,

When I process polygonal cells and calculate their cell area, I want to exclude the cells on edges, like this image:

CT4-1-1 1-1

Because these cell margins are tightly linked, so I can not exclude the outlines on edges by dilate, which will affect cell size.

Is there any idea to solve this issue?

Thanks a lot!

Justine Jiao at hzau.edu

ariel-waisman commented 2 years ago

Hi Justine Jiao, The current version of LabelsToRois does not include the option of removing the border labels before conversion into ROIs. However, there is a simple way to solve this. Starting from your label image, you can use the MorpholibJ plugin that comes with FIJI, go to Label Images / Remove Border Labels and remove all the labels from the Top, Bottom, Left and Right borders. You can then use this new label image to load it into LabelsToROIs.

Hope this solved this problem! Good luck! Ariel

Border Labels

JustineJiao commented 2 years ago

It works! Thank you very much! Justine