[ImageJ-devel] [icy] Re: .MRXS files in ICY

Wed May 1 17:25:02 CDT 2013

Hi Stephane,

> Thanks for the information.
> We are currently testing the following method to open image tile by tile:
>    byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
> 
> but it appears that all reader do not support it very well, we tested both 
> on JPEG and NDPI reader and obtained errors in both case.

> Is there any way 
> to know how much this method is supported ?

Your best bet is to ask on ome-devel and/or look at the open tickets:

http://trac.openmicroscopy.org.uk/ome/query?status=accepted&status=new&status=reopened&component=Bio-Formats&col=id&col=summary&col=status&col=type&col=priority&col=milestone&col=component&order=priority

In general, pretty much everything except for JPEG-based formats (JPEG,
NDPI, Hamamatsu VMS) will work in the latest stable version; for very
large images those won't work because the entire image needs to be
decoded in order to get a tile.  Support for NDPI and VMS is much better on
the develop branch (i.e.  trunk builds), but opening tiles from a JPEG still
requires that the entire image be decoded first.

Regards,
-Melissa

On Mon, Apr 29, 2013 at 09:09:37AM -0700, Stephane wrote:
> Hi Curtis,
> 
> Thanks for the information.
> We are currently testing the following method to open image tile by tile:
>    byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
> 
> but it appears that all reader do not support it very well, we tested both 
> on JPEG and NDPI reader and obtained errors in both case. Is there any way 
> to know how much this method is supported ?
> 
> Glad to hear about the IJ2 work on smart image disk caching, i am impatient 
> to see that in action :)
> 
> Cheers,
> 
> - Stephane
> 
> 
> Le lundi 29 avril 2013 17:40:21 UTC+2, Curtis Rueden a écrit :
> >
> > Hi Stephane & everyone,
> >
> > > We are also developing a plugin which may be used to split very large
> > > images in tiles but again we are very dependant to what the
> > > Bio-Formats library is able to do so it could be limited in some way.
> >
> > Bio-Formats provides an API for opening very large image planes in tiles:
> >
> >     byte[] openBytes(int no, int x, int y, int w, int h)
> >     byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
> >
> > Any valid tile width and height should behave correctly, but for optimal 
> > performance you can ask for the data's ideal tile size using:
> >
> >     int getOptimalTileWidth()
> >     int getOptimalTileHeight()
> >
> > So hopefully it would not be too difficult for Icy to provide a "crop 
> > image on import" sort of feature -- and maybe eventually a tile-based image 
> > viewer. Please let us know if you have any trouble with it!
> >
> > Regards,
> > Curtis
> >
> > P.S. This week, the ImageJ2 team will be working on the underpinnings in 
> > ImgLib2 for a SCIFIO-driven CellImg with intelligent disk caching. Once 
> > this work is ready, and if Icy becomes capable of using ImgLib2 data 
> > structures at the interface level, you could potentially harness this 
> > feature for tile-based image support.
> >
> >
> > On Mon, Apr 29, 2013 at 9:59 AM, Stephane <stephane.da... at pasteur.fr<javascript:>
> > > wrote:
> >
> >> Hi,
> >>
> >> Generally that type of microscope generate multi series image (with 
> >> different resolution) so even if Icy can't open the full resolution, you 
> >> should be able to open a sub resolution of the image.
> >> We are also developing a plugin which may be used to split very large 
> >> images in tiles but again we are very dependant to what the Bio-Formats 
> >> library is able to do so it could be limited in some way. Did you try to re 
> >> open your image with the last version of Bio-Format ? you should have 
> >> received an automatic update last friday.
> >>
> >> Cheers,
> >>
> >> - Stephane
> >>
> >>
> >> Le lundi 29 avril 2013 13:56:45 UTC+2, henrik aamodt a écrit :
> >>>
> >>>  Hi again, thank You for Your reply. Is there a quick way to reduce the 
> >>> X/Y in images, or has that to be done *before* importing them to ICY or 
> >>> maybe even when the slides are beeing scanned?
> >>>
> >>> sincerly
> >>> Henrik Aamodt
> >>> Oslo University Hospital
> >>> Norway
> >>>
> >>> Den 29.04.13 13:15, skrev Stephane: 
> >>>
> >>> Hi,
> >>>
> >>> 4 or 5 GB is really huge image, if the X/Y dimension is too large (> 
> >>> 32000x32000) then you may experience problems to open them.
> >>>
> >>> Le vendredi 26 avril 2013 22:00:16 UTC+2, Henrik Aamodt a écrit : 
> >>>>
> >>>>  hi, thanks for Your reply. we will be able to scan to .tiff soon, 
> >>>> that should resolve the issue. FYI the mirax files are aprox 4.5-5 GB, dont 
> >>>> have the x/y
> >>>>
> >>>>  henrik aamodt
> >>>> norway
> >>>>
> >>>> Den 26. apr. 2013 kl. 21:38 skrev Stephane <stephane.da... at pasteur.fr>:
> >>>>
> >>>>  Hello,
> >>>>
> >>>> Sorry for the delay !
> >>>> Actually mirax format is not yet supported by Bio-Formats (the library 
> >>>> we use to open image files) :
> >>>>
> >>>> http://www.openmicroscopy.org/**site/support/bio-formats/**
> >>>> supported-formats.html<http://www.openmicroscopy.org/site/support/bio-formats/supported-formats.html>
> >>>> http://trac.openmicroscopy.**org.uk/ome/ticket/4121<http://trac.openmicroscopy.org.uk/ome/ticket/4121>
> >>>>
> >>>> But at some point they will add support for it.
> >>>> From the error message we counld think your image is too big to be 
> >>>> laoded, do you know the size (X / Y dimension) of your image ?
> >>>>
> >>>> - Stephane
> >>>>
> >>>> Le lundi 22 avril 2013 19:38:00 UTC+2, hen... at broadpark.no a écrit : 
> >>>>>
> >>>>> Hi, anyone know a way to import .MRXS image files to ICY? I tried but 
> >>>>> got "image plane too large".  
> >>>>>
> >>>>>  thanks
> >>>>>
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