Input format

[yoser-alrawi]

Does the input file have to be in .czi?
Will any of the following formats work: .tiff , .jpg , .gci?

[jtalboom81]

Hi, I am not the author or creator, but I have been using this toolbox recently. The "rnascope_mouse.m" will process .tiff images (and I think the "rnascope_human" was coded for .tiff), and I assume other images formats; however, I would not ever use a .jpg (too much compression). Just be sure to uncomment line 20 (%out{1,2}.Dyes = {'Cy5','DsRed','EGFP','DAPI'}; %dye names are wiped out when cropped, and the channel names have no information) and add your dyes in the correct order. Loss of channel information is due to the loss metadata after conversion to .tiff from .czi. I hope this helps and good luck.

[yoser-alrawi]

Thank you for the reply. I am trying to use the "rnascope_mouse.m" workflow and that one is not coded for .tiff as I understood. I use the Keyence microscope and the raw images I get are in .gci. I also have the .tiff images. However, the .tiff images are large in number around 100. I tried inputting the raw image .gci as the filename in the rnascope_mouse command but I get error in the but I got the following error:
I also tried inputting the .tiff images as the filename in the rnascope_mouse command by selecting the folder name that contain those images, but I still got an error as shown below:

[yoser-alrawi]

I looked at the human rnascope tiff code and I understood that we can use it on mouse data as the lipofuscin channel can be left empty. So, I tried it on the tiff images I had but got the following error: