Importing whole slide images (from slides scanners)

[François-Xavier Frenois]

Dear all,

I'm playing with digital pathology and slides scanners (3DHISTECH, Philips, etc...).
Currently, and as far as I know, there's no way to import whole slide images in ICY. Also, unfortunately, there is still no "universal" open image format for these scanner devices...

I wonder if the dev team could implement an import option for the main WSI formats : .mrxs, .ndpi, .svs.

Thanks !

[Stephane]

Icy relies on the Bio-Formats library when it comes to open image files. Bio-Formats is able to recognize many different type of microscope images and some scanners formats as well. As far i know the NDPI is supported but not (yet) MRXS, i don't know about SVS though.

You can more informations about Bio-Formats here :
http://www.openmicroscopy.org/site/products/bio-formats

and the supported formats here :
http://www.openmicroscopy.org/site/support/bio-formats4/supported-formats.html

I think the mentioned formats have already been requested but you can still poke them about it (i can't find anymore the page where you can do that).

- Stephane

[Curtis Rueden]

Hi Stephane,

> As far i know the NDPI is supported but not (yet) MRXS, i don't know

> about SVS though.

Two tickets exist for tracking addition of MRXS support:

http://trac.openmicroscopy.org.uk/ome/ticket/4121

http://trac.openmicroscopy.org.uk/ome/ticket/11303

NDPI and SVS are both already supported:

http://openmicroscopy.org/site/support/bio-formats4/formats/aperio-svs-tiff.html

http://openmicroscopy.org/site/support/bio-formats4/formats/hamamatsu-ndpi.html

But I think just supporting the format is only the start of truly supporting HCS data. The slides are huge, often stored in a multi-resolution pyramid, and so data needs to be managed without reading the entire full-resolution planes at once. Visualization really needs a tile-based reader and viewer (e.g., like Google maps or Deep Zoom).

The OMERO clients have support for such "big images" with a tile-based viewer:

http://openmicroscopy.org/site/products/omero/big-images-support

Regards,

Curtis

--
You received this message because you are subscribed to the Google Groups "Icy imaging" group.
To unsubscribe from this group and stop receiving emails from it, send an email to icy-software...@googlegroups.com.
To post to this group, send email to icy-so...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/icy-software/0cfaef02-d6f5-4a9c-b795-df0f414a1954%40googlegroups.com.

For more options, visit https://groups.google.com/groups/opt_out.