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 > > <[email protected]<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 <[email protected]>: > >>>> > >>>> 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, [email protected] a écrit : > >>>>> > >>>>> Hi, anyone know a way to import .MRXS image files to ICY? I tried but > >>>>> got "image plane too large". > >>>>> > >>>>> thanks > >>>>> > >>>> -- > >>>> You received this message because you are subscribed to a topic in the > >>>> Google Groups "Icy imaging" group. > >>>> To unsubscribe from this topic, visit https://groups.google.com/d/** > >>>> topic/icy-software/**utQCSLMvr1Y/unsubscribe?hl=en<https://groups.google.com/d/topic/icy-software/utQCSLMvr1Y/unsubscribe?hl=en> > >>>> . > >>>> To unsubscribe from this group and all its topics, send an email to > >>>> icy-software...@googlegroups.**com. > >>>> To post to this group, send email to [email protected]. > >>>> To view this discussion on the web visit https://groups.google.com/d/** > >>>> msg/icy-software/-/**CrqZqyNHJAgJ<https://groups.google.com/d/msg/icy-software/-/CrqZqyNHJAgJ> > >>>> . > >>>> For more options, visit > >>>> https://groups.google.com/**groups/opt_out<https://groups.google.com/groups/opt_out> > >>>> . > >>>> > >>>> > >>>> > >>>> -- > >>> You received this message because you are subscribed to a topic in the > >>> Google Groups "Icy imaging" group. > >>> To unsubscribe from this topic, visit https://groups.google.com/d/** > >>> topic/icy-software/**utQCSLMvr1Y/unsubscribe?hl=en<https://groups.google.com/d/topic/icy-software/utQCSLMvr1Y/unsubscribe?hl=en> > >>> . > >>> To unsubscribe from this group and all its topics, send an email to > >>> icy-software...@**googlegroups.com. > >>> To post to this group, send email to [email protected]. > >>> To view this discussion on the web visit https://groups.google.com/d/** > >>> msg/icy-software/-/2YDns-**bhefAJ<https://groups.google.com/d/msg/icy-software/-/2YDns-bhefAJ> > >>> . > >>> For more options, visit > >>> https://groups.google.com/**groups/opt_out<https://groups.google.com/groups/opt_out> > >>> . > >>> > >>> > >>> > >>> -- > >> 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 [email protected] <javascript:>. > >> To post to this group, send email to > >> [email protected]<javascript:> > >> . > >> To view this discussion on the web visit > >> https://groups.google.com/d/msg/icy-software/-/l-yO979eP_MJ. > >> > >> For more options, visit https://groups.google.com/groups/opt_out. > >> > >> > >> > > > > > _______________________________________________ > ImageJ-devel mailing list > [email protected] > http://imagej.net/mailman/listinfo/imagej-devel _______________________________________________ ImageJ-devel mailing list [email protected] http://imagej.net/mailman/listinfo/imagej-devel
