czi images in Qupath

[i...@st-andrews.ac.uk]

Dear all,

I have opened a few czi images which have 4 channel IF images.

The one having one region scanned was kept its slide's ID, while the one having a few separate regions scanned was fragmented with random 'scene' numbers as you can see in the attached. So those fragmented ones are difficult to identify which is what.

I hope you can help me with this problem.

Thank you so much for your help.

Have a blessed day!

In Hwa

[Pete]

Unfortunately, QuPath v0.1.2 generates pretty useless thumbnail for most 16-bit images - it doesn't set the brightness/contrast in a sensible way.

This is fixed if you can install the beta version described at https://petebankhead.github.io/qupath/2018/03/19/qupath-updates.html (a bit more awkward, but instructions are at the bottom of the page).

The beta version also has the option of right-clicking on the thumbnail for an image that is open, and then updating it - so as to use the current display settings.  This means you can see better what it contains.  Unfortunately v0.1.2 doesn't have this option either, only the beta v0.1.3.

[Pete]

Upon re-reading this, I see that it's not just the thumbnail but also the name that is troublesome.  From memory, I think that this is also fixed in the beta version (if you use it when creating your project) - it not, please let me know.

[micros...@gmail.com]

In general for Zeiss images, multiple scenes are intended to be split using the Processing tab in Zen - "Split scenes (write files) option. Also, when setting up imaging experiments that generate multiple scenes, you should be able to label the scenes (instead of P1 P2 etc for multiple points), which can be included in the file names of the resulting split using one of the checkboxes. Hopefully the collection of split images can be imported into QuPath.

This can be done either at the microscope or using Zen Lite which is available for free (although "lite" is a bit of a misnomer with version 2.5 being over 6GB to download). You may be able to find a colleague who has already downloaded the installation file.

[Adal]

Where is the 'split scenes' options found? I am in the processing tab but I cannot see it - I'm using version 2.3.

[micros...@gmail.com]

It will be in the Utilities section, though you should be able to find it using the Search bar: