@@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
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.
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
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
Thank you for this tutorial. Very helpful!
Thank you so much! Really worked like a charm.
This is awesome! Thank you for the tips.
How could someone crop ROIs that are indifferent locations but make them the same size and also rotate/reorient them individually
did you figure it out? xx
@@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
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
did you figure it out? I'm struggling with the same thing right now
@@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.
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
Thank you so much! Just what I needed!
Thanks for the helpful video!!!!!!!!!!!!!!! Helps a lot!
thanks for your helpful video. Can we count the number of same objects like these grapes in ImageJ?
Thank you sir, very helpful for my GFP-brightfield-merged image series!
Thank you!
Hi, the video is very helpful, thank. But my images is passing too fast. How can I slow down it?
Do not play the image sequence. DO not push the triangle button
It does not recognize the images in windows, do you know how to solve it?
I'm going to name my first child CF Strock
excuse me sir. can you make video tutorial of image batch masking with fiji ? thankyouu
Is there any way to make a macro that can crop by intensity? I would like to crop images of plates into individual wells.
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