Hello, I have a H&E dataset which composed of 100 tile images (in tif format). These images are pre-processed before made publicly avaialble, that is, these images are in the same color space:
However, after I imported these images to QuPath, they appear to be in very different color spaces:
Is there any explanation why this problem happen and how to solve?
Thank you!
Can you provide a sample image, or check which Server is being used when you import them? Or possibly try changing which Server you select?
Thank you for your reply! I am using Bio-Formats the server type. Interestingly, if I change the image provider before importing the images, then the image will not appear in the Image List panel. I am not sure if I can share the image or not. Even though the image is publicly available, it requires registration still.
Well, good luck, will be hard to troubleshoot without any images.
The only thing I can think of is that whatever you were using to adjust the images before changed things like the brightness or contrast, which does not change the image at all. QuPath would have no idea what your display settings in another program were.
If this is the case, it should be possible to open the Brightness/Contrast setting in QuPath and reset it for all channels.
For some reason, the image has not been recognised as a standard RGB image – contrast isn’t normally adjusted automatically for RGB images in QuPath.
I tried reset the Brightness/Contrast setting and it still looked weird. I think it would be better to share one image but I am not sure how to do that.
I have seen people share images with DropBox, Box, GoogleDrive and similar. All of them should have free options if your files aren’t in the 15+GB range.
