Posted by
Aryeh Weiss on
Aug 11, 2016; 4:37am
URL: http://imagej.273.s1.nabble.com/images-contained-in-PDB-timelapse-files-tp5016990p5016998.html
Thanks to Curtis and Herbie for their quick replies.
I see that it is but the links to PDB file tool appear to be helpful.
On 10/08/2016 10:10 PM, Curtis Rueden wrote:
> Hi Aryeh,
>
> > The images that this system creates are apparently embedded in files
> > with the suffix ".pdb"
>
> It does not appear that Bio-Formats supports any file format with that
> extension, nor with the word "embryo" in the name anywhere. [1]
>
> It seems very likely this is a new proprietary file format which will
> need to be added to Bio-Formats. If you want to file such a request,
> then contact the OME community about it. [2] They will need at least
> one sample dataset. [3]
>
I cannot send real data, since it includes patient info. However, I have
asked for a "dummy" run to be done, so when next the instrument is
available I should be able to get a sample data file for you.
Best regards
--aryeh
> Regards,
> Curtis
>
> [1] See
>
https://www.openmicroscopy.org/site/support/bio-formats5.1/supported-formats.html;
> I also grepped the latest source code.
>
> [2]
https://www.openmicroscopy.org/site/community>
> [3]
http://qa.openmicroscopy.org.uk/qa/upload/ -- you can upload ZIP
> files.
>
> --
> Curtis Rueden
> LOCI software architect -
http://loci.wisc.edu/software> ImageJ2 lead, Fiji maintainer -
http://imagej.net/User:Rueden> Did you know ImageJ has a forum?
http://forum.imagej.net/>
>
> On Wed, Aug 10, 2016 at 1:42 PM, Aryeh Weiss <
[hidden email]
> <mailto:
[hidden email]>> wrote:
>
> I have been asked to work with timelapse image series which were
> created by a system called embryoscope.
> This is an incubator/microscope system that images times lapse of
> embryos created in-vitro.
>
> The images that this system creates are apparently embedded in
> files with the suffix ".pdb" (which makes is really hard to google
> for this image format because everything comes up "protein
> database"...)
>
> My guess is that this is a database file format that includes the
> images as well as patient metadata (based on the file size).
>
> Does anyone on this list know how to extract the raw image data
> from these files?
>
> There is a video export function, but it creates 500x500 jpg
> images, while the original images are 1280x1024 (and I hope are
> not jpg). There do not appear to be any options for changing this.
>
> Any pointers on this format will be greatly appreciated
>
> --aryeh
>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph: 972-3-5317638
> FAX: 972-3-7384051
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> <
http://imagej.nih.gov/ij/list.html>
>
>
--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel
Ph: 972-3-5317638
FAX: 972-3-7384051
--
ImageJ mailing list:
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