http://imagej.273.s1.nabble.com/Bio-Format-import-of-vsi-file-tp5012986p5012988.html
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”.
> 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.
>>
>>
>>
>>
>>
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http://imagej.nih.gov/ij/list.html>>
>
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