Issue with .vsi-files in QuPath

[ThiemoMMoellenkamp]

Hello there,

QuPath won't open my .vsi-images, which is a unique Olympus CellSens File-format.

Interestingly, Fiji is able to open these files with the bioformat-plugin, so, as the supported formats are same, I do not quite understand the reason. The Error Report is subsequently attached Does anyone have any idea on how to solve this issue?

Thank you so much in advance! Thiemo

Error Report: WARN: Unable to open /Volumes/LACIE SHARE/Doktorarbeit/Projekt_HIFLO/Demyelinisierung/APC/Alt2.vsi with OpenSlide: /Volumes/LACIE SHARE/Doktorarbeit/Projekt_HIFLO/Demyelinisierung/APC/Alt2.vsi: Not a file that OpenSlide can recognize WARN: Error opening /Volumes/LACIE SHARE/Doktorarbeit/Projekt_HIFLO/Demyelinisierung/APC/Alt2.vsi with ImageJ: Could not open /Volumes/LACIE SHARE/Doktorarbeit/Projekt_HIFLO/Demyelinisierung/APC/Alt2.vsi with ImageJ ERROR: Unable to build whole slide server - check your classpath for a suitable library (e.g. OpenSlide, BioFormats)

ERROR: /Applications/QuPath.app/Contents/Java/QuPathApp.jar:qupath/qupath-core-0.1.2.jar:qupath/qupath-core-awt-0.1.2.jar:qupath/qupath-core-processing-0.1.2.jar:qupath/qupath-core-processing-awt-0.1.2.jar:qupath/qupath-extension-ij-0.1.2.jar:qupath/qupath-extension-input-0.1.2.jar:qupath/qupath-extension-opencv-0.1.2.jar:qupath/qupath-extension-openslide-0.1.2.jar:qupath/qupath-extension-pen-0.1.2.jar:qupath/qupath-extension-script-editor-0.1.2.jar:qupath/qupath-gui-fx-0.1.2.jar:qupath/qupath-processing-ij-0.1.2.jar:qupath/qupath-processing-opencv-0.1.2.jar:jars/commons-math3-3.6.1.jar:jars/controlsfx-8.40.12.jar:jars/flowless-0.4.5.jar:jars/groovy-2.4.7.jar:jars/groovy-jsr223-2.4.7.jar:jars/gson-2.8.0.jar:jars/ij-1.51g.jar:jars/jfxtras-common-8.0-r5.jar:jars/jfxtras-menu-8.0-r5.jar:jars/jinput-2.0.6.jar:jars/jpen-2-150301.jar:jars/jutils-1.0.0.jar:jars/logback-classic-1.1.7.jar:jars/logback-core-1.1.7.jar:jars/opencv-3.1.0.jar:jars/openslide-3.4.1_2.jar:jars/packager.jar:jars/reactfx-2.0-M4u1.jar:jars/richtextfx-0.6.10.jar:jars/slf4j-api-1.7.20.jar:jars/undofx-1.2.jar:jars/wellbehavedfx-0.1.1.jar:QuPathApp.jar ERROR: Open image: Sorry, I can't open /Volumes/LACIE SHARE/Doktorarbeit/Projekt_HIFLO/Demyelinisierung/APC/Alt2.vsi

[melissalinkert]

It looks like you are using QuPath 0.1.2, which does not have Bio-Formats installed by default. Do you have the Bio-Formats extension (https://github.com/qupath/qupath-bioformats-extension) installed? If not, does installing that extension solve the problem?

[sbesson]

/cc @petebankhead

[petebankhead]

If you want to open the image with QuPath v0.1.2, you do indeed need the Bio-Formats extension. Documentation is here.

However, I'd recommend trying the latest milestone release of QuPath from https://github.com/qupath/qupath/releases - this may already have resolved any issues you see (in which case don't install the Bio-Formats extension - it isn't needed and isn't compatible with v0.2.0). Documentation for it is here.

I hope that a stable version of v0.2.0 will be available within the next month or so.

If Fiji can open the image with Bio-Formats, it is unlikely to be an issue with Bio-Formats. The image.sc discussion is probably a better place to follow up.

[sbesson]

Closing and using the image.sc thread as the single place of discussion as per https://forum.image.sc/t/importing-a-vsi-composite-image-in-imagej-via-bioformats-plugin-how-do-i-get-a-high-resolution-macro-image/35282/7