I have a set of rois that I’m using and I sometimes need to rotate them to match my images. I use the Selection Rotator tootl and I can see my roi rotate and can update the roi location in the ROIManager. However, when I go to save either the updated roi or even a new roi that’s rotated from the original, the rotation is gone. I’m using ImageJ 1.53i, can anyone assist me, please?
I cannot reproduce that issue.
- make a ROI
- add it to the ROI Manager [t]
- activate the ROI in the ROI Manager !!!
- activate the Selection Rotator and rotate/shift your selection
- press the update button in the ROI Manager !!!
- save the ROI
- reopen the ROI and it appears at the position where you saved it
That is at least what works for me.
Thank you for your reply. I’ve been doing some more troubleshooting and it may be specific to my rois, they’re more like overlays then selections of images. Here’s a link to them, they’re atlas image outlines that I’m trying to fit onto my microscope images: Atlas ROIs. I can rotate and save rois that are made in ImageJ but not these ones that are exported from other images.
I think I’m going to skip trying to save these rois and just flatten them onto what I need them on and then save that new image.
Ok, I see. Those really behave weird and I honestly would also not know how to solve that. I thing ImageJ is not really reading the files correctly as typical IJ ROIs.
You can try to add them to the image as overlay ( Image › Overlay › Add Selection…). If you then double click it, you can still rotate them and they should stay on the image as overlays. But they also seem to be limited inside the original rectangle, which might cut away some of the parts after rotation.
@Wayne and I developed the Selection Rotator.
I’ll have a look.
I have not seen such Rois before.
I’m not sure if your Rois are valid ImageJ Rois.
How did you create them?
Could it be that you have created your Rois via
Edit>Selection>Image To Selection ...?
In this case the answer can be maybe here in the ImageJ User Guide:
Creates an image selection (ImageROI). Image selections are Overlays↑ that can be moved around the canvas ( see Image▷Overlay▷Add Image…↓). Once created, opacity of the blended image can be re-adjusted at any time using Edit▷Selection▷Properties… [y]↑. Use
(Edit▷Selection▷Restore Selection [E]↑) to recover the blending image after clicking outside its limits. Use
(Flatten [F]↓) to finally embed the imageROI.
Note that image selections behave only partially as regular selections (e.g., can be added to the ROI Manager list, can be moved beyond image boundaries but cannot be resized or rotated). However they are stored in the TIFF header and can be saved and restored when saving images in TIFF format
Yes, I made the Rois by performing Image to Selection. Ok, that’s good to know they don’t function as normal Rois in terms of resizing or rotating, I will update my image analysis method.
Thank you so much for helping so quickly!