Hi, i am New in imagej and Hacer a question if could you answer please? İ am trying on one image that selecting multiple rois and want to for each roi apply crop, duplicate , add gray,Binary.......and skeletonise. Making it step bu step so bored. İ tried to make a macro but i failured. Can you help me please how can i handle. Thanks
Is there any way to use the second method where you manually select your region of interest but also ensure that the cropped images have the same dimensions. In this case they are all different sizes
@@kiarad2242 yes gotcha! What I do now is I select what I want to crop, then I go to edit -> selection -> specify. Then I specify the dimensions I want, then you can drag and move the box to the exact spot. Then press ctrl + x to crop I believe. I haven't got this to work as a macro, but I just do this individually to each image that I want to crop, but still be uniformly sized.
@@kiarad2242 Yes. Essentially it involves creating a rotated rectangle, moving and rotating over portion to keep, and then duplicating. The straighten command also works in place of duplicate, but I have a feeling it could technically cause distortion
Rather than cropping based on a user-specified ROI (as we review in this video), it sounds like something called "image segmentation" would be most suitable for your application. I am not sure exactly what information you are trying to extract from your images, but there may already be some plugins available for imageJ to read the intensity of wells in a plate. However, if you wanted to put together your own macro to pick out individual wells based on intensity, some thresholding method would probably be your best bet. I have some information that would be relevant for thresholding your images here: doi.org/10.5281/zenodo.5595203
