How to change file paths in a project for czi files with multiple images?

Hello,
I have a project on Qupath v0.1.2 for which my images (czi files) are stored on a shared drive. This has caused huge delays in image processing since working from home. I found this post which helped: https://github.com/qupath/qupath/issues/114
I thus created a copy of the project and reimported the images (after saving them locally on my computer) and image processing immediately improved in terms of speed.
However, most of my files have multiple images (scenes 0, 1,…) and for some reason it shows an error image when I try to reimport these locally saved files. I had no problem importing the files with a single image.
Is there any way around this?
Many thanks

Hi @clare,

What exact error message (and log message) is displayed when trying to open these images?

Also, would you consider updating your version of QuPath to 0.2.3? Many bug fixes and improvements were made since 0.1.2 and there might be a chance that your images will simply open with the last version of the software.

2 Likes

Hi @melvingelbard,
This is the message I get image
Unfortunately, all my analysis done so far has been on the old version so I would prefer to keep using that for maintaining consistency.
Thanks.

Hi @clare, can you add the log message (if any) from View → Show log?

Also, just to confirm: do you want to continue working with v0.1.2, or import images from v0.1.2 to work with them in v0.2? If you want to use v0.2, there’s a specific command File → Project… → Import images from v0.1.2 to help.

Finally, are all your images .czi? If so, I assume you’ve installed the old Bio-Formats extension (you need this with v0.1.2 but not v0.2).

1 Like

Hi @petebankhead,
Here’s what the log message shows:
WARN: Unable to open C:\Users\r01mpc17\Documents\New Oral Cavity Batch czi files\30-05-2019_RecognizedCode-16710.czi with OpenSlide: C:\Users\r01mpc17\Documents\New Oral Cavity Batch czi files\30-05-2019_RecognizedCode-16710.czi: Not a file that OpenSlide can recognize
WARN: Error opening C:\Users\r01mpc17\Documents\New Oral Cavity Batch czi files\30-05-2019_RecognizedCode-16710.czi with ImageJ: Could not open C:\Users\r01mpc17\Documents\New Oral Cavity Batch czi files\30-05-2019_RecognizedCode-16710.czi with ImageJ
INFO: Returning server: Bio-Formats for C:\Users\r01mpc17\Documents\New Oral Cavity Batch czi files\30-05-2019_RecognizedCode-16710.czi
ERROR: Project: Import images: TextArea@1ca90f9e[styleClass=text-input text-area]
INFO: Unable to import 1 paths:
C:\Users\r01mpc17\Documents\New Oral Cavity Batch czi files\30-05-2019_RecognizedCode-16710.czi

Also, yes I want to continue working with v0.1.2 and yes all my images are .czi and I added the Bio-Formats extension when I first started using Qupath.

If it helps, the qpdata files are 16710 Scene 0, 16710 Scene 1 ,etc while the czi files I am importing is 16710.czi. Don’t know if that makes a difference?
Thanks.

You mentioned the link/issue you were using, but not which solution. If you have not already tried Pete’s suggestion of editing the .qpproj file in a text editor, that might be the safer way to go in this case. It sounds like the multiple Scenes might be confusing things, and copying the entire project folder might be safer, if it was working well in the first place.

Generally, I would recommend splitting the scenes before importing the images into QuPath.

2 Likes

Hi @Research_Associate, I tried both the solutions and unfortunately neither worked.
When I opened the project file in notepad and edited the filepath to one of the scenes to a file saved locally, it showed an error message saying the project can’t be opened. I had to change the filepath back to the file from the shared drive.

I’m afraid I don’t know how to split the scenes before importing into Qupath, it usually does that for me when I import files into qupath.

QuPath is not splitting the scenes, it is showing you the scenes. Zen, the software that generates the CZI files and controls the microscope, generally has an option to Split Scenes (write files) in the Processing tab. That will give you each scene as an individual file and should be much easier to handle.

At least in the future.

Could you share that error? There might have been some problem with the editing of the file name. I am not sure why the file location change should matter if the file path was edited correctly, but I could be missing something.

You might also try creating the project from scratch in the new location, and then looking at the .qpproj file there for inspiration/exact text.

1 Like

I think it’s worth trying this again (and checking if there are any specific errors in the log… there might not be).

Note that the paths need to be exact, and on Windows you need to use either / or \\ – but not \ only.

So it should be something like

C:\\Users\\r01mpc17\\Documents\\New Oral Cavity Batch czi files\\30-05-2019_RecognizedCode-16710.czi

or else

C:/Users/r01mpc17/Documents/New Oral Cavity Batch czi files/30-05-2019_RecognizedCode-16710.czi

Note also that v0.1.2 may encode the scene name somewhere in the file path… although I don’t remember exactly how or where. This will need to be retained somehow.


Edit: From the checking the old code, I think it’s in the form

C:\\Users\\r01mpc17\\Documents\\New Oral Cavity Batch czi files\\30-05-2019_RecognizedCode-16710.czi::image-name

i.e. you’ll need to update the path, but retain the image-name part.

3 Likes

Hello,
Changing the file path worked! I think the error was that previously I wasn’t retaining the image name.
Thanks so much all!

1 Like