exporting mrxs format into regular image formats

[Sheng You]

Thanks so much. I tried to use VIPS to export mrxs images into tiff images.
It works very well on brightfield images. However, for fluorescent images,
the color of the exported images doesn't match the original color. You can
see these images from the link below. Fluorescence.tif is the screenshot
from Pannoramic Viewer which is a visualization tool for mxrs images.
Slide.tiff is the exported image using command line 'vips openslideload
--level 4 Fluorescence.mrxs slide.tiff[tile,compression=lzw]'. I wonder
this weird color is because of multiple channels of fluorescence images?
Brightfield is only one challenge and the export image looks good. For your
test mrxs data, you don't have fluorescent images.

https://www.dropbox.com/sh/au4r3h8p5xcgd5v/v3VvmG__lm?lst

Thanks.


On Wed, Mar 13, 2013 at 6:11 PM, Benjamin Gilbert <bgilbert at cs.cmu.edu>wrote:

> On 03/13/2013 08:27 PM, Sheng You wrote:
> > I came across openslide and wanted to know whether or not you
> > provide an open source or a software to export these mrxs format images
> > as regular format images with the resolution preserved.
>
> OpenSlide comes with a tool, openslide-write-png, which can export a
> slide region to a PNG.  If you want to produce a tiled TIFF of the
> entire slide, you can use VIPS:
>
>      https://github.com/openslide/openslide/wiki/OpenSlideAndVIPS
>
> --Benjamin Gilbert
>
> _______________________________________________
> openslide-users mailing list
> openslide-users at lists.andrew.cmu.edu
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>



-- 
Sheng You
Image Analysis Scientist

Presage Biosciences, Inc.****

530 Fairview Avenue North, Suite 1000****

Seattle, WA 98109****
206-995-8824 Ext. 823
sheng.you at presagebio.com
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