Open Microscopy Environment

Good morning everyone,

I am facing a problem with a proprietary version of the BigTIFF used by the Ventana scanner. We have a large dataset of WSI slide images, created with a Ventana iScan HT and saved in .bif format. We now need to automate analysis processing. It seems that any script/software relies on OpenSlide libraries, which indeed get caught into a bad striping artefact. The stripe components are not sticking correctly, with a significant disalignment. There is no reading issue with the Image Viewer by Ventana; however the viewer cannot convert .bif >> tiff (or any other format).

The issue with the Ventana modified BigTIFF is well known but apparently not solved
issue #132 OpenSlide ( https://github.com/openslide/openslide/issues/132 )

Any indication to solve the issue - aside rescanning a thousand slides - will be really appreciated.

Thank you very much in advance.

Nicole

Dear Nicole,

Unfortunately this particular format is not yet supported. We certainly have a growing backlog of many tens of new file formats, and Ventana BIF is amongst these - https://trello.com/c/oCH7PbA5/10-ventana-bif

Developing and testing new file format readers is significantly more costly than maintaining existing ones. Our priorities are necessarily our current academic deliverables (http://www.bbsrc.ac.uk/documents/2016-t ... d-grants/; https://wellcome.ac.uk/what-we-do/direc ... ple-funded), which do fund cross-platform resources for writing OME-TIFF (https://www.openmicroscopy.org/ome-files/) and support for several binary formats (BDV, etc.). While we certainly want to support as many formats as possible, the seemingly eternal development of new formats is hard to prioritise, given other pressing needs.

On the other hand, we will review any external contribution with new reader additions and consider their inclusion in a minor release of Bio-Formats. We have had several additions of this kind over the past few years and we always welcome independent community contributions to Bio-Formats as well (https://www.openmicroscopy.org/contributors/).

We are dedicated to maintaining Bio-Formats, but also, in the best spirit of open source development, sourcing contributions from the community for new formats.

Looking at the issue you mentioned for OpenSlide, the addition of the requirement to perform global tile registration in the absence of metadata which indicates the exact tile positions would appear to add a significant amount of work on top of adding a new reader. I will follow the OpenSlide progress with interest, since we would likely have to employ a similar strategy in order to implement a reader ourselves.


Kind regards,
Roger Leigh