I’m trying to open vsi files on the QuPath, but with no success unfortunately.
I already did what you all suggested here (creating a project) but didn’t work…I would like to know if you have some other suggestion.
The program version that I’m working with is the v0.2.2.
Thanks a lot!
We’d need more information about what exactly you’ve tried and if you saw any error messages – or, even better, a sample image if you can share one.
Also, what’s the source of the image (e.g. is a whole slide image from an Olympus scanner)?
Thank you so much for your answer, @petebankhead!
I’ll try to share here the error message I’m receiving. But it just says “Sorry, I can’t open the image…(file localization)”.
Yes, it’s a whole slide image from an Olympus scanner.
Is there any more info under View → Show log?
INFO: Initializing type adapters
INFO: Bio-Formats version 6.5.1
INFO: Loaded extension Bio-Formats server options (Bio-Formats 6.5.1) (46 ms)
INFO: Loaded extension Experimental commands (2 ms)
INFO: Loaded extension Experimental commands (51 ms)
INFO: Loaded extension ImageJ extension (161 ms)
INFO: Loaded extension JPen extension (45 ms)
INFO: Loaded extension Rich script editor extension (904 ms)
INFO: Loaded extension SVG export commands (3 ms)
INFO: OpenSlide version 3.4.1
INFO: Starting QuPath with parameters:
WARN: Temp memoization directory created at /var/folders/ws/7gw_rvcs0hs2lp1w3v97gdjc0000gn/T/qupath-memo-11953803386031607012
WARN: If you want to avoid this warning, either disable Bio-Formats memoization in the preferences or specify a directory to use
WARN: Missing expected .ets files in /Users/biancatroncarelli/Desktop/IPO:Kymab/QuPath/14019_13-5 PDL-1 (X40)
WARN: Unable to open UriImageSupport (class qupath.imagej.images.servers.ImageJServerBuilder) support=1.0, builders=1
ERROR: Error building server: Unable to build ImageServer for file:/Users/biancatroncarelli/Desktop/IPO:Kymab/QuPath/14019_13-5%20PDL-1%20(X40).vsi (args=) with requested provider qupath.imagej.images.servers.ImageJServerBuilder
ERROR: Open image: Sorry, I can’t open /Users/biancatroncarelli/Desktop/IPO:Kymab/QuPath/14019_13-5 PDL-1 (X40).vsi
Just this…It helps?
The key line seems to be:
I don’t encounter many VSI images, but I understand there is usually one file with extension .vsi and then a folder beside that which contains most of the data. That folder contains files with the extension .ets.
In your case, it looks like those .ets files are missing and so the image can’t be opened.
Okay! Got it!
And probably the .ets file is generated at the same time that the scan is being made right?
This .vsi file was sent to me by email…I’ll look the original file on the scan and then try to open again!
Thank you so much @petebankhead!
Yes, I think so. The folder that goes with the .vsi file is usually huge by comparison (e.g. the folder is > 1 GB but the .vsi file itself is a few MB).
It worked! Thank you so much!
And thanks for all support with QuPath, it’s an amazing tool!
Hey @petebankhead! I would like to make one more question.
I’m evaluating positive cell counting using the “positive cell detection” tool thought DAB positivity. It’s being great!
Is there some way to, hide the detected cells for a while, and them I could count the cells with positive membrane for another protein using the “counting” tool?
I don’t know if I made myself clear…it’s just because I’m looking for some way of counting two different proteins on the same ROI that I previously delimited using the annotations.
Thank you so much!!
Does toggling View → Show detections off do want you need (more easily accessed with the shortcut
D, or the button on the toolbar)?
It works perfectly!
Thanks again @petebankhead!
I’m doing the double stained cell analysis/counting following the workflow previously described.
Do you have some another suggestion of better methodology (in your opinion) that I can do it to keep working with QuPath and evaluate both proteins?
Hi @biancatroncarelli, I’d recommend starting a new thread and posting some example images. A lot will depend upon the specifics of your project.
2 posts were split to a new topic: VSI: missing expected .ets files