QuPath not opening .bif Z-stacks

Hi!
I used Ventana DP200 tissue scanner from Roche to digitalize several DAB slides. I performed Z-Stack scanning and obtained .bif images. Although Roche native software allows to visualize the images and their different optical slices in Z, no other program is able to open files in this format (.bif) or to show the Z-Stack options. Specifically, QuPath opens the files showing only one optical slice and doesn’t detect any other slice (showing always “series 0”). I tried importing with BioFormats, I tried FIJI, Huygens but none of them worked. I found a web viewer called PMA.start which is able to open these Z-Stacks, however, it does not allow to export good-quality snapshots. If anyone has an idea to open .bif whole slide images in QuPath I’ll be glad to hear it.

Hint: In PMA.start I discovered that each .bif file has a corresponding .tifp hidden file that is necessary to open the Z-stack properly.

https://docs.openmicroscopy.org/bio-formats/6.6.0/formats/ventana-bif.html
Openness seems low. Most Ventana files I have seen used were saved as .tif specifically to avoid the problems with .bif format. I have not seen Zstacks though, so not sure if non-bif formats are workable for those.

Maybe you could try converting them with the Glencoe tools - not sure.

I also have the .tif version of those files, but QuPath neither opens the Z-stack slicer.
I’ll try your suggestions. Thank you!

Hi @juliohr93, do you have a sample file which you would be able to share? The existing Bio-Formats reader is not currently aware of the tifp files so the Z stacks may not be supported yet.

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Hi @dgault! I share a .bif file and its correspondent .tifp under these links:

.tifp (6Kb): https://drive.google.com/file/d/1XTuPqiyy5kBX5pzVhtp3lxbfP6l_4vEn/view?usp=sharing

.bif (7Gb): GWIN2000337_608.bif - Google Drive

Unfortunately, I don’t have smaller files. I hope it helps to find a solution.

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Thank you, the sample files are always a great help in trying to reolve these issues. So am I correct in saying that each individual bif file is representing a single Z slice?

Thank you for asking and trying to help. No, each bif file contains the full stack of slices. Besides the native VENTANA software, PMA.start is the only software able to show the Z slicer in this kind of file. You can download PMA.start from here: https://free.pathomation.com/

Let me know if you have any questions and thank you once again.

I haven’t been able to get PMA.start working, how many slices are there supposed to be in the sample bif you provided?

There are 15 slices.

Thanks, I have created a Bio-Formats GitHub Issue to track this bug: Ventana BIF: Z stacks not supported · Issue #3678 · ome/bioformats · GitHub