I want to analyze fluorescent files with staining in 5 channels (4 + DAPI). In tutorials, people have multiple channels viewable in ‘Brightness and Contrast,’ but I only have RGB.
I attempted to install the QuPath Bio-Formats Extension (as explained here: GitHub - qupath/qupath-bioformats-extension: Extension to add Bio-Formats image support - **QuPath v0.1.2 only**) but when dragging the JAR files am met with ‘ERROR: Extension error: Unable to load Bio-Formats server options (Bio-Formats 6.5.1)’ and ‘ERROR: It is recommended that you delete file:/C:/Users/DavidJ/QuPath/extensions/qupath-extension-bioformats.jar and restart QuPath.’ I have deleted the extension and tried again to no avail.
Even if the image I am analyzing is multiplex TIFF added directly as the composite created in RNAscope HiPlex, the pixel type shows up as uint8 (RGB). I’m wondering if this is the problem but it seems like this is not something I can change (from what I gathered in these forums:
So how can I view more channels than RGB? To my understanding I can either do so via Bio-Formats (then how do I solve the extension error?) or simply cannot because the image is detected as RGB by the file reader. Please advise.