Re: images contained in PDB timelapse files

Posted by ctrueden on Aug 10, 2016; 7:10pm
URL: http://imagej.273.s1.nabble.com/images-contained-in-PDB-timelapse-files-tp5016990p5016993.html

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]

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.

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Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
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On Wed, Aug 10, 2016 at 1:42 PM, Aryeh Weiss <[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: [phone]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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