<div dir="ltr"><span style="font-family:arial,sans-serif;font-size:12.800000190734863px">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 '</span><span style="background-color:transparent;font-family:Consolas,'Liberation Mono',Courier,monospace;font-size:12px;color:rgb(51,51,51);line-height:19px">vips openslideload --level 4 Fluorescence.mrxs slide.tiff[tile,compression=lzw]</span><span style="font-family:arial,sans-serif;font-size:12.800000190734863px">'. 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. </span><div>
<br></div><div><font face="arial, sans-serif"><a href="https://www.dropbox.com/sh/au4r3h8p5xcgd5v/v3VvmG__lm?lst">https://www.dropbox.com/sh/au4r3h8p5xcgd5v/v3VvmG__lm?lst</a></font><br style="font-family:arial,sans-serif;font-size:12.800000190734863px">
<div style="font-family:arial,sans-serif;font-size:12.800000190734863px"><br></div><div style="font-family:arial,sans-serif;font-size:12.800000190734863px">Thanks.</div></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Wed, Mar 13, 2013 at 6:11 PM, Benjamin Gilbert <span dir="ltr"><<a href="mailto:bgilbert@cs.cmu.edu" target="_blank">bgilbert@cs.cmu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im">On 03/13/2013 08:27 PM, Sheng You wrote:<br>
> I came across openslide and wanted to know whether or not you<br>
> provide an open source or a software to export these mrxs format images<br>
> as regular format images with the resolution preserved.<br>
<br>
</div>OpenSlide comes with a tool, openslide-write-png, which can export a<br>
slide region to a PNG. If you want to produce a tiled TIFF of the<br>
entire slide, you can use VIPS:<br>
<br>
<a href="https://github.com/openslide/openslide/wiki/OpenSlideAndVIPS" target="_blank">https://github.com/openslide/openslide/wiki/OpenSlideAndVIPS</a><br>
<br>
--Benjamin Gilbert<br>
<br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><div style="margin:0px;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px">Sheng You</div><div style="margin:0px;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px">
Image Analysis Scientist<br></div><p style="margin:0px;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px">Presage Biosciences, Inc.<u></u><u></u></p><p style="margin:0px;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px">
530 Fairview Avenue North, Suite 1000<u></u><u></u></p><p style="margin:0px;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px">Seattle, WA 98109<u></u><u></u></p><font face="arial, sans-serif">206-995-8824 Ext. 823</font><div>
<a href="mailto:sheng.you@presagebio.com" target="_blank">sheng.you@presagebio.com</a></div></div>
</div>