[ome-devel] importing Hamamatsu-HIS files

[Roger Leigh]

On 14/05/2013 07:26, Grabmayr, Heinrich wrote:

> A colleague of mine is streaming movies from a Hamamatsu camera directly
> on hdd. When he uses the bio formats importer (ImageJ-plugin) to open
> these movies, every frame is opened as a new series, that is in a new
> window – when he clicks the option to open only one series, he is asked
> which one of series 1-N, N>>1 he wants to open. He was not yet able to
> open it ina window with a slider.

Dear Heinrich,

Looking at the code for HISReader
(https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats/src/loci/formats/in/HISReader.java)
the currently puts each image into a separate series; it always sets
sizeT=1.  This may be because we can't determine whether the images
belong to a timeseries, or are some other type of collection (e.g. a z
stack or tiles, etc.); I'll have to investigate that further.  If the
file format does contain sufficient metadata to determine that we are
dealing with a timeseries, then the reader can certainly be updated to
treat the data as a proper timeseries.

If you could possibly upload an example file to
   http://qa.openmicroscopy.org.uk/qa/upload/
then we can look at this in more detail.


Regards,
Roger

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096