ZVI Import issues

[David W. Robinson]

Hi there,

I have been trying to import .ZVI files but so far the images have all
been "corrupt". What happens is that portions of the image are tiling
and are not lining up correctly. I am getting a 3 layer stack, which I
would expect from a colour ZVI file, but have no clue whats going on
with this tiling. In Axiovision, should I save the files differently or
are there settings within ImageJ that I need to fiddle with to get
things all lined up? Any advice would be very welcome

Thank you in advance

David

--
David W. Robinson, Ph.D.
Assistant Professor
Center for Research on Occupational and Environmental Toxicology, L606
Senior Technology Advisor for Research and Education,
Provost's Office.
Oregon Health & Science University
3181 Sam Jackson Park Road
Portland OR 97239

Tel [phone]
Fax [phone]

[hidden email]

[ctrueden]

Hi David,

I assume you are using the ZVI plugin for ImageJ? Please note that it
was reverse engineered and may not work with all ZVIs. Try downloading
VisBio (http://www.loci.wisc.edu/visbio/) to see whether it properly
reads your files. If so, you can probably get ImageJ to read them
correctly by downloading the LOCI Bio-Formats package
(http://www.loci.wisc.edu/ome/formats.html) and adding the Apache
Jakarta POI (http://jakarta.apache.org/poi/) JAR file to your ImageJ
jre/lib folder (unless you are running Mac OS X, in which case the
process is different).

If your files do not work with VisBio or Bio-Formats, I would be very
interested in hearing about it, so that I can improve the ZVI support.

Thanks,
-Curtis

David W. Robinson wrote:

> Hi there,
>
> I have been trying to import .ZVI files but so far the images have all
> been "corrupt". What happens is that portions of the image are tiling
> and are not lining up correctly. I am getting a 3 layer stack, which I
> would expect from a colour ZVI file, but have no clue whats going on
> with this tiling. In Axiovision, should I save the files differently
> or are there settings within ImageJ that I need to fiddle with to get
> things all lined up? Any advice would be very welcome
>
> Thank you in advance
>
> David
>

[David W. Robinson]

Curtis,

Thanks for your quick response. I downloaded VisBio and did a
File>Import my zvi file and got the following error pop up in the error
console.

java.lang.NullPointerException
    at visad.data.tiff.TiffTools.bytesToInt(TiffTools.java:1196)
    at visad.data.bio.ZVIForm.initMetadata(ZVIForm.java:492)
    at visad.data.bio.ZVIForm.initFile(ZVIForm.java:480)
    at visad.data.bio.ZVIForm.getBlockCount(ZVIForm.java:351)
    at loci.visbio.data.ImageFamily.getBlockCount(ImageFamily.java:200)
    at loci.visbio.data.DatasetPane.buildPage(DatasetPane.java:387)
    at loci.visbio.data.DatasetPane$1.run(DatasetPane.java:246)

I am running on Windows XP. I am capturing the images with an AxioCam
and they are in color. They have been scanned at 3900 and each file is
~70MB in size.

I will let you know what happens with Loci

David


Curtis Rueden wrote:

> Hi David,
>
> I assume you are using the ZVI plugin for ImageJ? Please note that it
> was reverse engineered and may not work with all ZVIs. Try downloading
> VisBio (http://www.loci.wisc.edu/visbio/) to see whether it properly
> reads your files. If so, you can probably get ImageJ to read them
> correctly by downloading the LOCI Bio-Formats package
> (http://www.loci.wisc.edu/ome/formats.html) and adding the Apache
> Jakarta POI (http://jakarta.apache.org/poi/) JAR file to your ImageJ
> jre/lib folder (unless you are running Mac OS X, in which case the
> process is different).
>
> If your files do not work with VisBio or Bio-Formats, I would be very
> interested in hearing about it, so that I can improve the ZVI support.
>
> Thanks,
> -Curtis
>
> David W. Robinson wrote:
>
>> Hi there,
>>
>> I have been trying to import .ZVI files but so far the images have
>> all been "corrupt". What happens is that portions of the image are
>> tiling and are not lining up correctly. I am getting a 3 layer stack,
>> which I would expect from a colour ZVI file, but have no clue whats
>> going on with this tiling. In Axiovision, should I save the files
>> differently or are there settings within ImageJ that I need to fiddle
>> with to get things all lined up? Any advice would be very welcome
>>
>> Thank you in advance
>>
>> David
>>
>
>

--
David W. Robinson, Ph.D.
Assistant Professor
Center for Research on Occupational and Environmental Toxicology, L606
Senior Technology Advisor for Research and Education,
Provost's Office.
Oregon Health & Science University
3181 Sam Jackson Park Road
Portland OR 97239

Tel [phone]
Fax [phone]

[hidden email]