Opening Perkin Elmer Vectra scanner (.qptiff)

Hi all,
Recently I have been imaging several TMA slides with the Perkin Elmer Vectra scanner (.qptiff). At the moment I am trying to open them in ImageJ for setting a scale and to convert them to normal .tiff files (I suggested this should be possible in some way) since we want to analyse them in QuPath afterwards. I did instal the ImageJ bio-formats plugins, but somehow, even though the different combinations of settings that I have tried, my computer does not want to display the slides. Could you help me with this (e.g. which settings would you reccomend)? And if it is not possible to do the conversion in ImageJ, are there other programs that I can use?

Many thanks!


@ElsvS have you tried just opening the .qptiff image in QuPath directly? The latest milestone releases should support this immediately, including setting pixel size if necessary.


I agree, try using QuPath if you want to work there eventually.

It might be helpful to get imagej working though as well. To open a big .qptiff first open bioformats plugin:

Use the default settings next, but if you want to crop then check the “Crop on import” box like this.

qptiff images are in a pyramidal format. If the image is too big for your system pick one that has a lesser resolution:

last the crop on import window will appear.

all this can be scripted pretty easily. When I do a batch of images I have to open them and manually pick a ROI, but then I script saving it and going back and cropping the higher resolution image. -John

Indeed QuPath works for these images.
With the cropping option in ImageJ I somehow end up with black and white images. Usually this could be set in the import menu, but for these images it does not provide me any options for ‘color mode’.



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