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,
Yeah, other than the new Affine alignment option there’s no current method for rotating the images – sorry – but one could be added in the future. The use of RAW images is mostly a really convenient (and safe) process because it leaves the original completely unmolested.
I’d recommend you load the mspec image, rotate it manually, draw the ROIs, then rotate the ROIs back to the original orientation (and optionally the image). Then save the ROIs with the mspec. This way it shoudl all load up correctly.