Importing large Leica .lif images

[Claude Bonnard]

Dear all,

Does someone have experience with large (500k-1GB or more) .lif files?

I use the last LOCI plugin in a ImageJ Version 1.37v, running on a 64bit
Windows system with Java JDK1.6.0.
The opening start with LOCI Formats Import Option, as I would expect, and I
tried two options (Merge Channels to RGB ans open each channel in its own
window) and the result is the same:
1)-Analyzing,
2) read thumbnail for serie (1,2,3..88 or so)
3) Info box stating that the file is not a TIFF, JPEG, GIF, etc..

This .lif file is the result of a mosaic made under a Leica microscope, which
save it as one huge file.

If someone want to try this, I can make on of this file available..

Thanks for your advice

Claude

--
Claude Bonnard Ph.D.
ISREC (Swiss Institute for Experimental Cancer Research)
Microscopy, Imaging and Morphology Core Facility [MIM]
Lab F216
Ch des Boveresses 155
CH-1066 Epalinges
Switzerland
email: [hidden email]
phone: [41-21]-692-5891
  fax: [41-21]-652-6933

[Fabrice Cordelières]

Dear all,

We have just experienced the same problem as previously reported (LOCI
plugin not opening lif files anymore) !
However, this does not appear to come from the size of the image but rather
from the file format: LOCI plugin can still open "old" dataset (taken prior
to the confocal software update, LAS-AF version 1.5.1), but is not able to
open images taken with the new version of the confocal software (LAS-AF
version 1.6.0 build 1016).
I hope this comment will help developers solving the problem.


Fab


Fabrice Cordelières, PhD
 
Institut Curie - Section de recherche/ CNRS UMR 146
Plateforme d'Imagerie Cellulaire et Tissulaire
Bâtiment 112 - Centre universitaire
91405 Orsay Cedex
FRANCE
 
Tél. : [phone]
Fax. : [phone]

-----Message d'origine-----
De : ImageJ Interest Group [mailto:[hidden email]] De la part de Claude
Bonnard
Envoyé : lundi 5 mars 2007 14:14
À : [hidden email]
Objet : Importing large Leica .lif images

Dear all,

Does someone have experience with large (500k-1GB or more) .lif files?

I use the last LOCI plugin in a ImageJ Version 1.37v, running on a 64bit
Windows system with Java JDK1.6.0.
The opening start with LOCI Formats Import Option, as I would expect, and I
tried two options (Merge Channels to RGB ans open each channel in its own
window) and the result is the same:
1)-Analyzing,
2) read thumbnail for serie (1,2,3..88 or so)
3) Info box stating that the file is not a TIFF, JPEG, GIF, etc..

This .lif file is the result of a mosaic made under a Leica microscope,
which
save it as one huge file.

If someone want to try this, I can make on of this file available..

Thanks for your advice

Claude

--
Claude Bonnard Ph.D.
ISREC (Swiss Institute for Experimental Cancer Research)
Microscopy, Imaging and Morphology Core Facility [MIM]
Lab F216
Ch des Boveresses 155
CH-1066 Epalinges
Switzerland
email: [hidden email]
phone: [41-21]-692-5891
  fax: [41-21]-652-6933

[ctrueden]

Hi Claude & Fab,

We are very interested in updating Bio-Formats to handle the new LIF
version and fix any bugs. If you could make some sample data available
to us, it would be extremely helpful in improving the software. If you
need somewhere to put the data I can pass along our FTP server
information; just let me know.

Thanks,
Curtis

On 3/5/07, Fabrice Cordelières <[hidden email]> wrote:

> Dear all,
>
> We have just experienced the same problem as previously reported (LOCI
> plugin not opening lif files anymore) !
> However, this does not appear to come from the size of the image but rather
> from the file format: LOCI plugin can still open "old" dataset (taken prior
> to the confocal software update, LAS-AF version 1.5.1), but is not able to
> open images taken with the new version of the confocal software (LAS-AF
> version 1.6.0 build 1016).
> I hope this comment will help developers solving the problem.
>
>
> Fab
>
>
> Fabrice Cordelières, PhD
>
> Institut Curie - Section de recherche/ CNRS UMR 146
> Plateforme d'Imagerie Cellulaire et Tissulaire
> Bâtiment 112 - Centre universitaire
> 91405 Orsay Cedex
> FRANCE
>
> Tél. : [phone]
> Fax. : [phone]
>
> -----Message d'origine-----
> De: ImageJ Interest Group [mailto:[hidden email]] De la part de Claude
> Bonnard
> Envoyé: lundi 5 mars 2007 14:14
> À: [hidden email]
> Objet: Importing large Leica .lif images
>
> Dear all,
>
> Does someone have experience with large (500k-1GB or more) .lif files?
>
> I use the last LOCI plugin in a ImageJ Version 1.37v, running on a 64bit
> Windows system with Java JDK1.6.0.
> The opening start with LOCI Formats Import Option, as I would expect, and I
> tried two options (Merge Channels to RGB ans open each channel in its own
> window) and the result is the same:
> 1)-Analyzing,
> 2) read thumbnail for serie (1,2,3..88 or so)
> 3) Info box stating that the file is not a TIFF, JPEG, GIF, etc..
>
> This .lif file is the result of a mosaic made under a Leica microscope,
> which
> save it as one huge file.
>
> If someone want to try this, I can make on of this file available..
>
> Thanks for your advice
>
> Claude
>
> --
> Claude Bonnard Ph.D.
> ISREC (Swiss Institute for Experimental Cancer Research)
> Microscopy, Imaging and Morphology Core Facility [MIM]
> Lab F216
> Ch des Boveresses 155
> CH-1066 Epalinges
> Switzerland
> email: [hidden email]
> phone: [41-21]-692-5891
>   fax: [41-21]-652-6933
>