slidebook file format issues

[alexia ferrand]

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Dear all,
 
In our facility in Basel, we are frequently using a 3i
spinning disk microscope. While the system itself performs extremely well and
our users are happy with the acquisition process, things become much more
complex as we get into photomanipulation analysis.
 
So far, we have advised our users to save their data in
the proprietary slidebook file format (that's the software shipped by 3i for
acquisition and analysis), which could be opened with the latest versions of
Imaris and more recently with Fiji. However, since last month we cannot use
Fiji anymore, the slidebook file format is not read properly, even using the
latest stable version of the LOCI plugin. The issue has been reported and will
be changed for the subsequent release. The LOCI team advised us to use the
OME-TIFF export function in the slidebook software. This file format is
helpful, by keeping the metadata and the properties of the initial data.
 
However, when we tried to save our files as OME-TIFF and
open them in Fiji, we end up with individual files for each channel and
timepoint...
Just like usual TIFF files, but with an extra text file
containing the metadata.
 
When using Imaris to read the proprietary slidebook
format, the files open as expected, but it cannot process the ROIs stored in
there. We are aware of the community's recognition of the problem with such
work by the SciJava group and their effort to provide a common set of ROI types
which will be usable in all image analysis programs. (See http://www.scijava.org/roi-model/roi.html#model-toplevel).
But unfortunately this is not available yet.
 
We could use the OME-TIFF and reorder the
channels/timepoints to reconstruct the files as movies, but we have the feeling
that we will still lose the information for the ROIs anyway. The ROIs could be
manually re-created, and the data analysed in Fiji, but this is adding extra steps
and introduces inaccuracy by the manual part.
 
The other option will be to use the slidebook software to
do the whole analysis. It is easy to have the FRAP curves visualization and the
analysis done there. However, with the slidebook software we have then only
been able to save the intensity values. This means that the analysis has to be
redone from scratch, which is extremely frustrating... We are considering
writing a matlab script for it, but we were wondering if such a script already
exists somewhere?
 
We are interested to know if anyone has encountered such
issues and managed to find any other suitable workarounds?
 
Best,
Alexia
 
------------------------------------
Dr Alexia Ferrand
Imaging Core Facility
Kragenbau,
Room G1055
Klingelbergstrasse
50 / 70
CH-4056
Basel
 
Office:  [phone]
Email: [hidden email]

[samuel connell]

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*****Appropriate Commercial Response******

Dear Alexia,

We are glad to hear that you are happy with your 3i system. In the big
picture, I'd like to invite you as a user of one of our systems in the
world to feel free to always email [hidden email] with
your software or hardware inquiries. Our team of Application Scientists,
physicists, hardware & software engineers, will all be happy to lend a hand
in working through any issues you may be encountering.

That being said, we have have been working directly with the BioFormats
team to ensure that this plugin for Fiji or ImageJ works seamlessly with
SlideBook files. If I'm not mistaken, this is intended to be implemented in
the upcoming 4.5 release:

http://trac.openmicroscopy.org.uk/ome/ticket/9543

We'll be glad to work with you on assisting you with executing your FRAP
analysis within SlideBook as well. Additionally, you likely are aware of
this already, but within SlideBook itself, you can execute matlab routines
directly.

I will also follow up off-list from our [hidden email] to
engage the resources of our entire team.

Kindest Regards,
--
Sam

------------------------

Samuel A. Connell

Senior Applications Scientist

Intelligent Imaging Innovations, Inc

Office: [phone] x6926

[hidden email]

On Wed, Nov 7, 2012 at 8:24 AM, alexia ferrand <[hidden email]>wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear all,
>
> In our facility in Basel, we are frequently using a 3i
> spinning disk microscope. While the system itself performs extremely well
> and
> our users are happy with the acquisition process, things become much more
> complex as we get into photomanipulation analysis.
>
> So far, we have advised our users to save their data in
> the proprietary slidebook file format (that's the software shipped by 3i
> for
> acquisition and analysis), which could be opened with the latest versions
> of
> Imaris and more recently with Fiji. However, since last month we cannot use
> Fiji anymore, the slidebook file format is not read properly, even using
> the
> latest stable version of the LOCI plugin. The issue has been reported and
> will
> be changed for the subsequent release. The LOCI team advised us to use the
> OME-TIFF export function in the slidebook software. This file format is
> helpful, by keeping the metadata and the properties of the initial data.
>
> However, when we tried to save our files as OME-TIFF and
> open them in Fiji, we end up with individual files for each channel and
> timepoint...
> Just like usual TIFF files, but with an extra text file
> containing the metadata.
>
> When using Imaris to read the proprietary slidebook
> format, the files open as expected, but it cannot process the ROIs stored
> in
> there. We are aware of the community's recognition of the problem with such
> work by the SciJava group and their effort to provide a common set of ROI
> types
> which will be usable in all image analysis programs. (See
> http://www.scijava.org/roi-model/roi.html#model-toplevel).
> But unfortunately this is not available yet.
>
> We could use the OME-TIFF and reorder the
> channels/timepoints to reconstruct the files as movies, but we have the
> feeling
> that we will still lose the information for the ROIs anyway. The ROIs
> could be
> manually re-created, and the data analysed in Fiji, but this is adding
> extra steps
> and introduces inaccuracy by the manual part.
>
> The other option will be to use the slidebook software to
> do the whole analysis. It is easy to have the FRAP curves visualization
> and the
> analysis done there. However, with the slidebook software we have then only
> been able to save the intensity values. This means that the analysis has
> to be
> redone from scratch, which is extremely frustrating... We are considering
> writing a matlab script for it, but we were wondering if such a script
> already
> exists somewhere?
>
> We are interested to know if anyone has encountered such
> issues and managed to find any other suitable workarounds?
>
> Best,
> Alexia
>
> ------------------------------------
> Dr Alexia Ferrand
> Imaging Core Facility
> Kragenbau,
> Room G1055
> Klingelbergstrasse
> 50 / 70
> CH-4056
> Basel
>
> Office:  [phone]
> Email: [hidden email]
>