Lossless Mirax image file conversion/size reduction

Ryan Murray ryan.z.murray at helsinki.fi
Tue May 5 09:27:11 EDT 2015


In our lab we generate a lot of Mirax (mrxs) images of slides, and we  
are currently researching ways in which we can compress the images as  
much as possible (reduce file size) while still maintaining high  
quality at higher resolutions.

I've looked into a tool called JP2 WSI Converter  
(http://jvsmicroscope.uta.fi/?q=jp2wsiconverter), which claims to be  
able to convert Mirax to JPEG2000 in a 'lossless' manner.  
Unfortunately I could not get this tool to work on sample mirax slides  
from the Openslide web server demo page, but the existence of this  
tool suggests that converting Mirax to JPEG2000 is a good strategy to  
reduce file size while maintaining quality.

To tried to cobble together my own Mirax to JPEG2000 conversion using  
openslide/vips) by doing:

vips openslideload --level 1 input.mrxs output.tiff[tile,compression=lzw]

and then converting the tiff to a jp2 file using imagemagick.

While this worked, the problem is that the size was only reduced by  
about 40% and it was not a 'lossless' conversion, i.e. there was a  
clear loss of quality at higher resolutions.

My question is: Is there a way to perform a 'lossless' conversion of a  
mirax image in a manner analogous to how a WAV might be converted to  
an MP3 (even thought the file size is much smaller for an MP3, the  
sound quality is practically indistinguishable from a WAV to the human  

Alternatively, if there is another approach of which I'm not aware  
that could accomplish this goal, we would definitely be interested in  
hearing about it.

Thanks so much for your time!

Take care


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