Re: FIJI thinks my greyscale image stack is a coloured image?

Posted by Mr_Sonky on Aug 08, 2014; 1:05am
URL: http://imagej.273.s1.nabble.com/FIJI-thinks-my-greyscale-image-stack-is-a-coloured-image-tp5009051p5009067.html

Hi all,

 From LIM Soon Yew John (IMB),"Are you using FIJI (ImageJ2)? If yes, you can try to turn off the SCIFIO under Edit>Options>ImageJ2. I encounter an issue that FIJI (ImageJ2) did not open my RGB image correctly but it works again after I turn off SCIFO. Another thing that you can try is go to Image>Hyperstacks>Stack to Hyperstack..., set the correct number of slices and channel."

firstly, thank you John, I had not realised that SCIFIO opening the files was the problem. Your solution worked right off the bat  Actually, the first thing I tried was turning it into a hyperstack and specifying the colour but that did not work.

From Mark Hiner-2,"I just wanted to add that this recommendation is also in the bug reporting best practices <http://imagej.net/Bug_reporting_best_practices#Disable_SCIFIO>, with the
caveat that disabling SCIFIO is a temporary workaround. These bugs should
still be reported, as they will need to be resolved eventually."

Yes Mark, I have read that turning off SCIFIO was the first troubleshooting step. I now realised that I have stumbled upon a "bug" whereas previously I thought the problem was myself - I simply thought I was doing something wrong and choosing the wrong options in FIJI. I was annoyed more at myself rather than at the program.

From dscho ,"The best way to make sure that your grayscale images are read correctly is
to be friendly to the people who you ask to work for you, free of cost, and follow the excellent instructions provided here: http://imagej.net/Bug_reporting_best_practices" 

I am really sorry I have offended where I genuinely wanted to seek help. I will in the future avoid expressing disappointment and not use words like "annoying". I have left my original post unedited as an example of how not to approach for help in a public forum. As I said, I did not realise that I have stumbled upon a bug. I will report it via FIJI>Help>Report a Bug as soon as I can. Thank you for referring the above mentioned guides .