images contained in PDB timelapse files

[Aryeh Weiss]

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

[ctrueden]

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.

--
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]> 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
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Herbie]

Good evening Aryeh Weiss,

did you have a look at:
<https://en.wikipedia.org/wiki/Program_database>

which is a bit confusing as well but you may try the mentioned
extraction tools.

Here is a different link:
<http://www.online-convert.com/file-format/pdb>

HTH

Herbie

:::::::::::::::::::::::::::::::::::::::::
Am 10.08.16 um 20:42 schrieb Aryeh Weiss:

> 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
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Aryeh Weiss]

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: [phone]
>
>     --
>     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: [phone]


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html