Software to open bif images

Hi all,

Do you know a software that can open bif images (from Roche/Ventana scanners) ? (or at least convert them into standart tiff).
A few months ago, I used to open them with Fiji or QuPath (at least, I could open a croped image), but now I have an error (loci.formats.FormatException: Unsupported overlap direction: LEFT). Is it due to some changes in the fio-format plugin ?

Thanks for your answers

Nico

Ventana scanners can save in several different ways, so while it may be due to a change in BioFormats (you could try several different versions with QuPath 1.2/1.3 since you can manually add or remove different BioFormats versions) it may also be due to changes in how the file is saved. If you are the only user, though, that likely isn’t the case. Have you tried the old images that used to work?

You could try uploading a sample image to the BioFormats support site, or if the image is too large, request an upload link.

I have had issues with different types of files saved from Ventana scanners, sometimes I have to force BioFormats to read the extension, and it works, and other times I have to force BioFormats not to read the extension and it works with OpenSlide. I don’t recall seeing that particular error, though.

Hi @Research_Associate,
Thanks for your reply.
It’s both my old and new files that are failing.
When you say :

How do you force Bio-format to read or not the extension ? (here, I renamed my .bif in .tif otherwise it didn’t accepted it)

I’ll try first to play with QuPath. But if I have the “stable” version on my computer, changing the bio-format in the milestone versions will also change it in my stable version ? Right ?

OpenSlide is a c library isn’t it ? Which environnement do you use ? (In an earlier life, I used to program my algorithms in c, but I remember it was a nightmare to configure everything : libtiff, libxml, ligjpeg, bigtiff…)

Nico

In the preferences, near the bottom (once you have the BioFormats plugin added), you can list the file extensions you want to include or exclude.

The stable release accesses the Extensions folder (or whatever you set as the extensions folder in the Preferences) to look for a copy of BioFormats. The milestone versions have one built in, but also doesn’t default to assigning any extensions folder at all. I am not sure you can change BioFormats in a milestone without rebuilding.

Attempting to force some of the milestones to use an extensions folder that contained a BioFormats plugin caused “bad things.” I’m not sure if this is still the case in m4.

I’m not really a programmer, just learned a little scripting, and pretty much only use QuPath in Windows. For many of these formats, QuPath will default to Openslide when BioFormats is prohibited. If Openslide is expected to work.

In the milestone versions, BioFormats is included by default. The good news is that you should be able to change the version for v0.1.2 independently without trouble (it’s in your extensions directory).

I believe that bif support only came to BioFormats very recently, so I presume OpenSlide was being used before then.

In v0.2.0-m4 there’s finally an option to specify which reader you want to use when adding an image to a project, so you don’t need to leave it up to QuPath to decide for you whether it will use OpenSlide or BioFormats. You can even add the same image twice using different readers to compare, and QuPath should be able to handle them separately without getting confused.

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