I have been handed some images for analysis which is great! Unfortunately almost all of them are sideways or upside down (why? I have no idea!). There is no problem in generating a multispectral image, but things get complicated when I rotate the image and save ROIs. When i reload the images the ROIs are in the wrong spot because the image loads sideways again. If I save the rotated image, as a tif the .mspec doesn’t find it and image doesn’t load. Similarly, if I save the rotated image over top of the RAW file, the .mspec can’t find the image. So I guess my question is, can I: generate .mspec, rotate the image, define the ROIs and then save the image and have it reload the correct way up with the ROIs aligned? Or do I have to open each of the the RAW files in a different program and rotate them, save them, and then generate .mspec?
I have a similar issue with my images. I open the .mspec, rotate the image ( Image -> transform -> rotate (tick both boxes) -> save the rotation angle in a .txt file with the .mspec and the image), draw my ROIs and save them (ROI manager -> more -> save). When I open the .mspec, I rotate it by that same angle so that when I reload the ROIs everything matches up. That’s how I navigate that issue. I haven’t tried what you propose at the end, mostly because I’m not sure how to save the file as a RAW again after rotating it in another program so that the ‘load multispectral image image’ function works, but also because I want to make use of the small file size of the .mspec rather than having to create huge .tiff files. I wouldn’t be surprised if a more elegant solution exits without having to create large image files though, curious.
I hope this helps,