[ome-devel] MATLAB Class for fast and simple writing of OME-TIFFs

[Sebastien Besson]

Hi Gary,

thank you very much for your email.
Regarding the code itself, I had a quick glance at it and did not see any obvious issue so far. Obviously part of it is
quite specific to your application but there are many methods useful for the community and it is really nice to see
concrete examples of usage.

A couple of immediate thoughts:
- are you happy with your current hybrid solution? The performance issue arising with Bio-Formats only calls is
  certainly something we want to investigate but this will require a bit of time. Having access to the code allows us
  to schedule this in our agenda thought.

- I am considering porting back some of this code back to the open-source code. In particular the mechanisms
  for creating and linking annotations to images could likely be simplified for others by adding helper methods, e.g.
  something like:

>> tagID = createTagAnnotation(metadata, value);
>> linkImageAnnotation(metadata, imageIndex, tagID);

Would that be acceptable for you and if so do you have any comments/suggestions?

Thanks again for sharing your code,
Sebastien

On 31 Oct 2014, at 21:09, Yellen, Gary <gary_yellen at hms.harvard.edu<mailto:gary_yellen at hms.harvard.edu>> wrote:

Hi all –
Here is some code for exporting OME-TIFFs from MATLAB data, using a combination of Bio-Formats calls for the metadata and MATLAB Tiff calls for the actual file writing.  I have found the speed to be significantly faster than using all Bio-Formats calls.

I’ve also included tools (hopefully general!) for adding all different types of annotations to the images, without wrestling with the many Java calls necessary to do this.

The main code is the OMETiffWriter_gy class, in a single file.  There’s documentation of the workflow at the top of the code.  I’ve also included example code in the dF_saveAsOMETiff.m file, which is just for your perusal since it requires object classes that are peculiar to our lab.

Please let me know if you find bugs in the OMETiffWriter_gy code, or if you make improvements.

Best,
Gary


Gary Yellen, PhD  ::   Professor of Neurobiology
Harvard Medical School :: 220 Longwood Ave [WAB 328] :: Boston, MA 02115
617-432-0137 ::  gary_yellen at hms.harvard.edu<mailto:gary_yellen at hms.harvard.edu>


<OMETiffWriter_gy.m><dF_saveAsOMETiff.m>

Dr Sébastien Besson
Open Microscopy Environment / Harvard Medical School
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
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