General question on Orbit 3.64 + Can I do intensity quantification like the Aperio Imagescope does?

Dear allm

I am new on Orbit and I am using V3.64 on my Macbook. One thing I noticed is the windows, e.g. Feature Configuration, cannot be resized and therefore some buttons are hidden e.g. I can only see Disable and Stain 1 for the Color Deconvolution Stain function.

Another question is can I do intensity quantification based on the classes defined in the classification step? e.g. measure the intensity of the DAB stain in tumor cells without segmentation because I am interested in the overall stain. I reckon I can export to CellProfiler for analysis but it is not clear to me how to do it.

Cheers

Dear @HYKY ,
you can, but it not really recommended. The idea in Orbit is to quantify the area of staining (positive class), not the intensity.

If you really want to do so you can go in the feature config (F3), activate the “Features/Histogram” option for your channel of interest and then process the quantificaiton in batch mode(!).
this will output you the histogram (intensity counts per 1,…,255 bin) which you could export and analyze.

Regards,
Manuel

Dear @mstritt ,


Thanks for the reply. Please see my screenshot below. I am using Orbit 3.64 on my macbook and open .svs images in my local disk.
I cannot see “Feature/histoogram” in the Feature config tab and as you may notice, some lines are chopped with only the upper part of the characters are shown. I cannot expand the window (in case some tabs are hidden?). Is that a bug?

Another thing is when I try to open a file within Orbit, I cannot see my files in the directory where compatible image files locate (see the second photo)

Therefore, I cannot use the Batch mode to analyse the intensity.
My aim is to measure the intensity of the whole tissue and report the % area of low/med/high staining.

What would you recommend here? I now try to reinstall Orbit and see if it helps. Thank you.

Hi just downloaded and extract it again. Nothing has changed.