Login  Register

Re: Bio-Format import of .vsi file?

Posted by Mark Hiner on May 29, 2015; 7:21pm
URL: http://imagej.273.s1.nabble.com/Bio-Format-import-of-vsi-file-tp5012986p5012987.html

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