Where does "Reconvolve standard stains" option go in v0.2.x?

In qupath v0.1.x, there’s option to adjust stain vectors, and Reconvolve standard stains which changes the color of the whole slides. I know this is just for visual, but I can vow for it usefulness. For example, for 5 unknown cases, with default color out of the box, I can read 2/5, when changing to new color with Reconvolve standard stains option, I can read the rest 3 much easier.
Slides were scanned with Roche Ventana scanner, Roche uPath software also show the slide colors which are similar to qupath after Reconvolving the colors.
Please bring this option back in new v0.2 version. Or am i missing something?

See here for what I mean by Reconvolve standard stains:


Thank you!

1 Like

Interesting, I hadn’t heard that Reconvolve standard stains was being used.

Since all commands in the software take effort to maintain, and potentially add to the complexity of the user interface and documentation, one of my goals currently is to try to remove any that aren’t worth this effort - making it easier to add new features and improve the software overall. I have faint memories of removing ‘Reconvolve standard stains’ some time ago, although I don’t recall when since I don’t think anyone else has mentioned it to me since then…

I’ll give this some more thought. In general, I am keen to reduce the dependency on color deconvolution where possible, since my impression is that this can lead to confusion - and I would prefer other deterministic color transforms that don’t depend upon specific settings (here, the stain vectors and background values).

The one that comes to mind is that under Edit → Preferences… there is an option Gamma value that applies to the viewer (and actually remains even when different windows are opened). Can this be used to achieve a similar effect?

If so, I’ll look at trying to make the option more accessible (e.g. through the Brightness/Contrast dialog). If not, are you able to provide any screenshots showing the difference achieved with reconvolving using standard stains?

1 Like

Hi Pete, thanks for reaching back!
Yes, I’ll send you some pictures later to show how Reconvolving the stains makes things different. We just use the whole slide scanning more with Ventana scanner recently. There’s Roche Upath web-based viewer coming with the scanner, my co-workers just used it at work. They also tried qupath before, or still using, and all acknowledged that the colors on qupath is totally from Roche Upath, they either abandon using qupath, or only 1 co-worker still try to hang on with qupath but feeling colors ain’t the way he likes. In recent unknown cases discussion, we found out that changing qupath color will make things easier to read. With some extra effort, I tried to fix the issue to bring qupath into usefulness at our institution, I came across a tutorial from Drexel:https://drexel.edu/medicine/about/departments/pathology-laboratory-medicine/advanced-pathology-imaging-laboratory/zarella-lab/h-e-histology-color-normalization/qupath/
trying to normalize the colors. This is tedious involving setup and Matlab (extra licensing).

When I read the qupath instruction, I found there was the option called “Reconvolve standard stains”, and voila, just simple step can fix the whole headache, I’m trying to show my co-workers around again and they start coming back to qupath, but question is always “why using older version?” where the same option goes in newer version? is there any better way to do it?
I always have to bear in mind that they are doctors (MD, PhD), not in digital medicine field, hence need a quick button, not a whole setup and scripts.