How to convert czi. into one single plane tiff. in QuPath

My images are in czi. and I’m able to open them in QuPath with Bio-format installed, but I found that I could only work with one single plane at a time, like cell detection. To solve this issue, I open czi. in FIJI first and convert the czi. image into tiff. and then open the tiff. with QuPath and do image analysis. That works but not convenient enough. I didn’t find any online sources talking about this issue. Can anybody help me? I really appreciate it!

Hi @Hinhin,

I’m a little confused on how converting the file to .tiff allowed you to work with more than one plane. Could you possibly mean that you created some sort of Z-Projection in FIJI? Or that you saved one slice?


Hi @Hinhin,

I suppose that you mean a plane of a z-stack here.
You can do the conversion in QuPath in two ways:

  1. Use the File > Export images… > OME-TIFF
    And then choose the parameters that you want the image to be exported with.
  2. If you have the last version of QuPath (QuPath-m10), which was just released today, you can use the command line interface to convert an image and specify all the parameters in the command line, e.g.

qupath convert-ome -z [z-slice number] path/to/your/czi/file path/to/output/file.ome.tif


  • convert-ome is the command to convert an image to OME-TIFF.
  • -z [z-slice number] indicates which z-slice(s) to include in the conversion (default=‘all’, you can change this to a single number (e.g. 3) or a range (e.g. 2-5), the ranges are inclusive).
  • path/to/your/czi/file is the full path to the file you want to convert.
  • path/to/output/file.ome.tif is the full path where you want to see you converted image created. Careful that the directory must exist to avoid errors.

There are many more parameters that you can use when calling convert-ome. To see a full list, you can type in your terminal:
qupath help convert-ome

Additionally, you can prompt a general help message in your terminal to get some guidance about the command line interface. Just type:
qupath help

Personally, I recommend using the second option (using the terminal), as it allows easy changes with parameters and is easy to apply on different images consequently. Please tell us how it goes! :slight_smile:


Sorry that I didn’t make it clear enough. I converted czi (z-stack) into tiff. in FIJI by doing “z-project”, so that I can work with the whole image when I open tiff. with QuPath. While in QuPath, I can only work with one single plane of the z-stack at a time. My question is how I can do what I did in FIJI with QuPath so that I don’t need to go back and froth from FIJI and QuPath.

Perform the max intensity projections in Zen before going to QuPath. You can have a flattened CZI file that way with all of the metadata intact for future inspection.

Also, the Z-project function is available through the ImageJ built into QuPath. If the entire image can be opened in FIJI, I suspect the same could be done through an ImageJ script in QuPath, though you might have to grab each slice one at a time (through script). Even if you did this, though, you would be creating images which you would then need to add into a new project, or add back into the same project. It would not modify the current image in the project.