Bio-Format import of .vsi file?
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Bio-Format import of .vsi file?
 
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I have a Java plugin that reads .vsi files using the Bio-Format importer:
//run Bio-Formats Importer on that file, taking the defaults IJ.run("Bio-Formats Importer", "open=" + dir + filename + " autoscale color_mode=Custom view=Hyperstack stack_order=XYCZT" + " series_1 series_0_channel_0_red=0 series_0_channel_0_green=255" + " series_0_channel_0_blue=0"); I believe that this worked recently (within the last 6 months) but now fails (note: I’m not completely sure of this behavior on exactly the same file - I’m working on that). The current behaviour is that there is a Stack with exactly 3 images. Two are identical, and look like like a reasonable single slice (in Green). The third and last slice in the stack is solid BLACK. Help, please! -- Kenneth Sloan [hidden email]<mailto:[hidden email]> Vision is the art of seeing what is invisible to others. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Bio-Format import of .vsi file?
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Hi Kenneth,
>I believe that this worked recently (within the last 6 months) You can download older versions of Bio-Formats[1] to test this. Probably the easiest thing would be to download the command line tools[2] from various releases, so you can test the behavior with pure Bio-Formats - comparing metadata with showinf, or display with ijview, should be helpful here. The 5.0.8 and 5.1.0 split seems like a probable culprit. If that's no help you can always use their bug reporting system[3] - including uploading sample data for them to look at. But note that there is an OME users conference next week, so the team may not be able to respond immediately. Best, - Mark [1] http://downloads.openmicroscopy.org/bio-formats/ [2] http://www.openmicroscopy.org/site/support/bio-formats5.1/users/comlinetools/ [3] https://www.openmicroscopy.org/site/support/bio-formats5.1/about/bug-reporting.html On Fri, May 29, 2015 at 1:58 PM, Kenneth R Sloan <[hidden email]> wrote: > I have a Java plugin that reads .vsi files using the Bio-Format importer: > > //run Bio-Formats Importer on that file, taking the defaults > IJ.run("Bio-Formats Importer", "open=" + dir + filename > + " autoscale color_mode=Custom view=Hyperstack > stack_order=XYCZT" > + " series_1 series_0_channel_0_red=0 > series_0_channel_0_green=255" > + " series_0_channel_0_blue=0"); > > > I believe that this worked recently (within the last 6 months) but now > fails (note: I’m not completely sure of this behavior on exactly the same > file - I’m working on that). > > The current behaviour is that there is a Stack with exactly 3 images. Two > are identical, and look like like a reasonable single slice (in Green). > The third and last slice in the stack is solid BLACK. > > Help, please! > > -- > Kenneth Sloan > [hidden email]<mailto:[hidden email]> > Vision is the art of seeing what is invisible to others. > > > > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Bio-Format import of .vsi file?
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Thanks - I’m still trying to nail down documentation that it’s a Bio-Formats problem. It’s still possible (likely, even) that this is a “customer problem”.
-- Kenneth Sloan [hidden email] Vision is the art of seeing what is invisible to others. > On May 29, 2015, at 14:23 , Mark Hiner <[hidden email]> wrote: > > Hi Kenneth, > >> I believe that this worked recently (within the last 6 months) > > You can download older versions of Bio-Formats[1] to test this. Probably > the easiest thing would be to download the command line tools[2] from > various releases, so you can test the behavior with pure Bio-Formats - > comparing metadata with showinf, or display with ijview, should be helpful > here. The 5.0.8 and 5.1.0 split seems like a probable culprit. > > If that's no help you can always use their bug reporting system[3] - > including uploading sample data for them to look at. But note that there is > an OME users conference next week, so the team may not be able to respond > immediately. > > Best, > - Mark > > [1] http://downloads.openmicroscopy.org/bio-formats/ > [2] > http://www.openmicroscopy.org/site/support/bio-formats5.1/users/comlinetools/ > [3] > https://www.openmicroscopy.org/site/support/bio-formats5.1/about/bug-reporting.html > > On Fri, May 29, 2015 at 1:58 PM, Kenneth R Sloan <[hidden email]> wrote: > >> I have a Java plugin that reads .vsi files using the Bio-Format importer: >> >> //run Bio-Formats Importer on that file, taking the defaults >> IJ.run("Bio-Formats Importer", "open=" + dir + filename >> + " autoscale color_mode=Custom view=Hyperstack >> stack_order=XYCZT" >> + " series_1 series_0_channel_0_red=0 >> series_0_channel_0_green=255" >> + " series_0_channel_0_blue=0"); >> >> >> I believe that this worked recently (within the last 6 months) but now >> fails (note: I’m not completely sure of this behavior on exactly the same >> file - I’m working on that). >> >> The current behaviour is that there is a Stack with exactly 3 images. Two >> are identical, and look like like a reasonable single slice (in Green). >> The third and last slice in the stack is solid BLACK. >> >> Help, please! >> >> -- >> Kenneth Sloan >> [hidden email]<mailto:[hidden email]> >> Vision is the art of seeing what is invisible to others. >> >> >> >> >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Bio-Format import of .vsi file?
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As predicted - “customer error”. “never mind”
-- Kenneth Sloan [hidden email] Vision is the art of seeing what is invisible to others. > On May 29, 2015, at 14:53 , Kenneth R Sloan <[hidden email]> wrote: > > Thanks - I’m still trying to nail down documentation that it’s a Bio-Formats problem. It’s still possible (likely, even) that this is a “customer problem”. > > -- > Kenneth Sloan > [hidden email] > Vision is the art of seeing what is invisible to others. > > > > >> On May 29, 2015, at 14:23 , Mark Hiner <[hidden email]> wrote: >> >> Hi Kenneth, >> >>> I believe that this worked recently (within the last 6 months) >> >> You can download older versions of Bio-Formats[1] to test this. Probably >> the easiest thing would be to download the command line tools[2] from >> various releases, so you can test the behavior with pure Bio-Formats - >> comparing metadata with showinf, or display with ijview, should be helpful >> here. The 5.0.8 and 5.1.0 split seems like a probable culprit. >> >> If that's no help you can always use their bug reporting system[3] - >> including uploading sample data for them to look at. But note that there is >> an OME users conference next week, so the team may not be able to respond >> immediately. >> >> Best, >> - Mark >> >> [1] http://downloads.openmicroscopy.org/bio-formats/ >> [2] >> http://www.openmicroscopy.org/site/support/bio-formats5.1/users/comlinetools/ >> [3] >> https://www.openmicroscopy.org/site/support/bio-formats5.1/about/bug-reporting.html >> >> On Fri, May 29, 2015 at 1:58 PM, Kenneth R Sloan <[hidden email]> wrote: >> >>> I have a Java plugin that reads .vsi files using the Bio-Format importer: >>> >>> //run Bio-Formats Importer on that file, taking the defaults >>> IJ.run("Bio-Formats Importer", "open=" + dir + filename >>> + " autoscale color_mode=Custom view=Hyperstack >>> stack_order=XYCZT" >>> + " series_1 series_0_channel_0_red=0 >>> series_0_channel_0_green=255" >>> + " series_0_channel_0_blue=0"); >>> >>> >>> I believe that this worked recently (within the last 6 months) but now >>> fails (note: I’m not completely sure of this behavior on exactly the same >>> file - I’m working on that). >>> >>> The current behaviour is that there is a Stack with exactly 3 images. Two >>> are identical, and look like like a reasonable single slice (in Green). >>> The third and last slice in the stack is solid BLACK. >>> >>> Help, please! >>> >>> -- >>> Kenneth Sloan >>> [hidden email]<mailto:[hidden email]> >>> Vision is the art of seeing what is invisible to others. >>> >>> >>> >>> >>> >>> -- >>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >>> >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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