I recently upgraded to the newest version of Fiji for Mac and now am having a problem saving images that can be seen by other programs. Formerly I would process an image in Fiji and to save it so that I could view it easily on my Mac and easily import into PS or ppt I would flatten the image and save as a tif. Now when I try to flatten the image I get an error message about overlay or selection required. And if I just proceed to save as a tif the image is only black in my finder window and when I try to open it in PS it’s black on black. Any suggestions?
Flatten does 2 things:
- Burn the scale bar or other overlay onto the image
- Convert the image to RGB.
So if you don’t have an overlay, Image > Type > RGB Color will do step 2, giving you a TIFF in a format that Preview, Photoshop, & PowerPoint can display.
This behavior was introduced by a recent commit from June 13. With earlier versions, the Flatten command simply created an RGB image when there was no overlay present.
It’s up to @Wayne’s discretion whether this is considered a regression or an intended change in ImageJ 1.x behavior.
This happens if you save 16-bit images that are autoscaled in ImageJ but will be displayed at their 0-65535 intensity range in other programs such as Finder and Photoshop. See here for more info regarding image types in ImageJ.
The regression that caused the Flatten command to not work with non-RGB images when there was no overlay or ROI present is fixed in the latest ImageJ daily build (1.51e36).