FAO anyone using Becker & Hickl .sdt TCSPC files & OMERO.
Posted: Thu May 09, 2013 9:32 amAs some of you may be aware, our group at Imperial College, London has been working on making our toolset for processing & viewing
Fluorescence Lifetime Imaging (FLIM) data compatible with OMERO.
One of the issues is that Time-resolved Fluorescence Lifetime data involves a second time dimension (t) in addition to the real-time dimension (T) provided by the standard 5D OME model.
The addition of extra dimensions is supported by OMERO as described in
http://www.openmicroscopy.org/site/supp ... orage.html.
Unfortunately the importer for Becker & Hickl .sdt Time Correlated Single Photon Counting (TCSPC) files predates the introduction of this solution & currently encodes the extra (t) dimension into C[hannel].
It would be possible to simply amend the importer to to add the ModuloAlongC XmlAnnotation described in the link without further changes.
However, we strongly believe that a number of issues of future compatibility with other modalities can be avoided by standardising on the use of one dimension for FLIM.
We also believe that the chosen standard for FLIM should be ModuloAlongT (i.e. encoding the extra t dimension into T[ime]
We would therefore like to propose two changes to the existing importer for Becker & Hickl .sdt TCSPC files:
1) Encode the time-bins into the T dimension rather than C as now.
2) Add the ModuloAlongT xml annotation as described in the link.
For any person or group currently using this file type, change 1) would have the disastrous effect of creating two different types of images in OMERO
from the same file imported with different versions of the importer.
So if anyone has either existing software or a workflow that involves this file type & would be adversely affected by these changes please let us know.
Many thanks.
Fluorescence Lifetime Imaging (FLIM) data compatible with OMERO.
One of the issues is that Time-resolved Fluorescence Lifetime data involves a second time dimension (t) in addition to the real-time dimension (T) provided by the standard 5D OME model.
The addition of extra dimensions is supported by OMERO as described in
http://www.openmicroscopy.org/site/supp ... orage.html.
Unfortunately the importer for Becker & Hickl .sdt Time Correlated Single Photon Counting (TCSPC) files predates the introduction of this solution & currently encodes the extra (t) dimension into C[hannel].
It would be possible to simply amend the importer to to add the ModuloAlongC XmlAnnotation described in the link without further changes.
However, we strongly believe that a number of issues of future compatibility with other modalities can be avoided by standardising on the use of one dimension for FLIM.
We also believe that the chosen standard for FLIM should be ModuloAlongT (i.e. encoding the extra t dimension into T[ime]
We would therefore like to propose two changes to the existing importer for Becker & Hickl .sdt TCSPC files:
1) Encode the time-bins into the T dimension rather than C as now.
2) Add the ModuloAlongT xml annotation as described in the link.
For any person or group currently using this file type, change 1) would have the disastrous effect of creating two different types of images in OMERO
from the same file imported with different versions of the importer.
So if anyone has either existing software or a workflow that involves this file type & would be adversely affected by these changes please let us know.
Many thanks.