http://imagej.273.s1.nabble.com/Bio-Format-import-of-vsi-file-tp5012986p5012995.html
As predicted - “customer error”. “never mind”
> 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.
>>>
>>>
>>>
>>>
>>>
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>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>>
>>
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