Segmentation newbie help thresholding segmentation

Hi, I am ultra new to FIJI and tried to threshold segment my Zeiss SEM tiff image after opening with Bio-format command. All I get is a error stating “composite images cannot be thresholded” and the threshold box shows no pixel intensities as shown in the screenshot. I have tried converting the image to 8 bit Grayscale but cannot change it. Is there anyone please who can launch me in the correct direction?
Many thanks in advance
image

Hi @Sugardady,

the image you want to segment looks a bit strange: usually, there is no Zeiss logo in images which come from the micrsocope :wink: Is this image from a website or a presentation?

Try to safe the images at the microscope in format LSM, CZI or TIF. Afterwards, opening in ImageJ and applying thresholds should just work.

Cheers,
Robert

1 Like

Dear Haesleinhuepf (Robert); Many thanks for your reply. I guess you are advising me that it is not the correct technically because fiji will interrogate those pixels as well. Also regarding etiquette it is not normal practice to retain the information bar at the bottom of my images. Otherwise the Zeiss SEM saves the Tiff images with this info bar automatically.

It is a long learning curve but I have worked out that my original tiff RGB images should first be duplicated without the info bar then converted to tiff 8 bit images then auto thresholded so hopefuly I am now on the correct path.

Thanks so much

Tschuss
Sugardady