*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****
*****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 [log in to unmask] 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 [log in to unmask] to
engage the resources of our entire team.
Kindest Regards,
--
Sam
------------------------
Samuel A. Connell
Senior Applications Scientist
Intelligent Imaging Innovations, Inc
Office: (303) 607-9429 x6926
[log in to unmask]
On Wed, Nov 7, 2012 at 8:24 AM, alexia ferrand <[log in to unmask]>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: +41 (61) 267 22 50
> Email: [log in to unmask]
>
|
