Hi Irum Abbasi,

it is very difficult to explain ImageJ in a post here on ResearchGate. I would recommend you to look for tutorials on youtube (or something similar). As ImageJ is used so much, there are many great tutorials and guides out there.

If you have a very specific question, you could also ask in this forum (https://forum.image.sc/) which is specifically for all kind of images and image analysis and has it's own tag for ImageJ.

Good luck with ImageJ!

Selene

Thank you so much Dear Selene Lickfett

Hi there. ImageJ is very easy to use, so do not worry. I use this tool for neuroscience imaging in neurons as well by the way. First of all, i would start with youtube tutorials. Maybe you would need to acquire microscopic images where you have the ones with direct illumination and the ones with only fluorescence. The final result should be merging them in order to point out where the fuorescence is being expresswd. Am i right?What will you do is basically extract all the colors out of the images in the 3 basics colors and then, you should retain your color of choice. For example, if you are going to use red labeled neurons like the mcherry aav labeled neurons, you will only retain the red mask. The you gonna merge the red mask with the regular image. On youtube or imagej forum you will find exactly this guide step by step. If you need any further info feel free to ask

Cheers

Thank you so much Enzo Cancedda