*****
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]
|
