Converting Whole Slide Images to OME-TIFF: A New Workflow

Glencoe Software and the OME team are pleased to announce a new collection of command line tools [1,2,3] for converting whole slide images from proprietary file formats into pyramidal OME-TIFF; an open file format. These tools were initially designed to convert Philips’ iSyntax and 3DHISTECH’s .mrxs file formats, but can also be used with any other whole slide format supported by Bio-Formats.

A full writeup can be found on the Glencoe Software blog here:

https://www.glencoesoftware.com/blog/2019/12/09/converting-whole-slide-images-to-OME-TIFF.html

We look forward to your feedback and comments. Our thanks to InnovateUK for the support that made this work possible.

[1] https://github.com/glencoesoftware/isyntax2raw
[2] https://github.com/glencoesoftware/bioformats2raw
[3] https://github.com/glencoesoftware/raw2ometiff

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We have updated the blog post today to acknowledge additional support from iCAIRD and PathLAKE.