BoneJ- Inverse foreground calcultaion

Hi everyone. I am a new user and I encountered a basic issue. I am using BoneJ to calculate BV/BT, Tb.Th and Tb.Sp of binary imported image sequence that are created in Matlab. The problem is the plugin is calculating aforementioned parameters for the background of my image:


According to the image options, foreground color is white and background color is black.

I really appreciate your help.

Best regards,
Mahtab

Please check your look-up table: it looks to me that you have a LUT which is displaying foreground in black and background in white. If you hover your cursor over black and white regions and check the status bar you will see that the pixel values change. BoneJ uses the ImageJ convention that 0 is background and 255 is foreground and ignores the LUT, which are colours for display purposes only.

Thank you Micheal. My image is a binary matrix of 0 and 1 digits. I tried Image > Lookup Tables > Invert LUT and the problem is solved now.
Thanks for your hint.

0 and 1 should not work as a binary image in ImageJ. You may have to multiply by 255 to convert the 1s to 255s. Alternatively set and apply a threshold that splits 0 and 1.

Thank you Micheal for your quick answer. I made the change on the matrix, now I have a binary matrix of 0 and 255 digits.
The problem is that based on the matrix, I create binary image slices to import them as a image sequence in BoneJ and create my geometry there again. There should be a more straightforward way to import the binary matrix directly to ImageJ that I don’t know. I appreciate your comment on this topic. Thanks a lot.

There is a connector between Matlab and ImageJ, which might help if you have a lot of images to pass between the two systems.

Thank yo so much for your support.
I’ll try it.