Opening Volocity files

[Jeremy Sanderson]

Dear Listers,

 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?

Thanks,
Jeremy

[Kurt De Vos-2]

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.
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.
kurt

On 12 Feb 2007, at 14:43, Jeremy Sanderson wrote:

> Dear Listers,
>
> 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?
>
> Thanks,
> Jeremy



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[Michael Schell]

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).

2.  Export as .liff and then use the LOCI Bioformats importer to  
import .liff.  This works sometimes, and not others.

To my knowledge, there is no means to directly  open Volocity format  
files directly into ImageJ



On Feb 12, 2007, at 9:43 AM, Jeremy Sanderson wrote:

> Dear Listers,
>
> 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?
>
> Thanks,
> Jeremy

[ctrueden]

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

[Kurt De Vos-2]

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

[ctrueden]

Hi Kurt,

Thank you for the details on the Volocity format. We are looking into
whether adding support to Bio-Formats is feasible.

Also good to hear about your Openlab LIFF plugin. Have you considered
folding your improvements back into Bio-Formats? We would welcome any
contributions!

The advantage would be that not only would your fixes work within
ImageJ, but also other libraries that use Bio-Formats: VisBio, OME,
VisAD, and hopefully others as time goes on. Moreover, the ultimate
goal of Bio-Formats is to provide a framework for metadata conversion
from any supported third-party format into a standard format
(OME-XML). This strategy will enable universal easy access to common
metadata such as Z and T dimensions, physical pixel sizes (i.e.,
calibration), excitation wavelength and source, lens magnification,
additional hardware information, and more. *steps off soapbox*

Cheers,
Curtis

On 2/13/07, Kurt De Vos <[hidden email]> wrote:

> 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
>