Re: Opening Volocity files

Posted by Kurt De Vos-2 on
URL: http://imagej.273.s1.nabble.com/Opening-Volocity-files-tp3700330p3700333.html

Hi, Curtis

My Openlab Liff plugin is not using bio-formats (although i did use  
some code from it).
It is basically a translation of the Improvision Openlab C-code, and  
opens the Liff5 format,
some versions of IFF2 are also supported.
I'll post it to Wayne after i clean up the code a bit.

The new volocity format is a metakit database, and there is no public  
info on it that i can get from Improvision.
So they recommend reading the exported tiffs.
And i don't think there is a java api for metakit available, so would  
would have to use JNI.

Kurt

On 13 Feb 2007, at 15:33, Curtis Rueden wrote:

> Hi Jeremy, Kurt & Michael,
>
> On 2/12/07, Jeremy Sanderson <[hidden email]> wrote:
>>  Can anyone please tell me if there is a plugin for opening Volocity
>> files in ImageJ, and where I can get this if it exists?
>
> Jeremy, I do not know anything about the Volocity format. Is it
> distinct from Openlab LIFF, and Openlab RAW? If so, what is the file
> extension? Is it something that would be worthwhile for us to add to
> Bio-Formats? Could you provide any sample data?
>
> On 2/12/07, Kurt De Vos <[hidden email]> wrote:
>> I wrote a plugin that opens Volocity files, but only when they are
>> exported as tiffs.
>> Basically it opens the tiff using the standard ImageJ opener and then
>> reads the
>> volocity specific tags (time; calibration) using the
>> loci.formats.TiffTools.
>
> Kurt, I'm glad the Bio-Formats library is useful to you. If you have
> any suggestions for improvements, please let us know.
>
>> If you are interested i can send you a copy.
>> I also have a plugin that opens Openlab LIFF files if that can  
>> help you.
>
> Are you talking about Bio-Formats, or some other plugin for Openlab
> LIFF? I was not aware of any others. Have you considered listing it on
> the ImageJ Documentation Wiki's "Which file formats are supported by
> ImageJ" page?
> http://imagejdocu.tudor.lu/imagej-documentation-wiki/faq/which-file- 
> types-are-supported-by-imagej
>
> On 2/12/07, Michael Schell <[hidden email]> wrote:
>> Your options for opening Volocity files on ImageJ are:
>>
>> 1.  Export as .tiff and use the Improvision importer plugin (can be
>> found in the ImageJ bundle complied by Tony Collins).  This will
>> import the images and the scale info (but not timestamp).
>
> I think this is the Improvision TIFF importer plugin that I wrote. The
> code is very simple; timestamp would most likely be very easy to add.
>
>> 2.  Export as .liff and then use the LOCI Bioformats importer to
>> import .liff.  This works sometimes, and not others.
>
> Michael, if you have LIFF files that do not work well for you, please
> feel free to send them to us. This goes for anyone with data files in
> any supported format -- please contact us so that we can make
> Bio-Formats better!
>
>> To my knowledge, there is no means to directly  open Volocity format
>> files directly into ImageJ
>
> It sounds like this file format is separate from Openlab LIFF and RAW.
> Any chance I could obtain some samples, so that we can look into
> adding it to Bio-Formats?
>
> Thanks,
> Curtis