[ome-users] Retrieving Stage Position in DV Files (more details)

[Sebastien Besson (Staff)]

Hi Alex,

thanks for the detailed information, would it be possible for you to upload a sample file where
the stage position is currently missing from Bio-Formats at
http://qa.openmicroscopy.org.uk/qa/upload/ ?


The DeltaVision reader uses two different strategies for reading the stage positions depending
on the presence of a log file and the number of series [1] [2]. It might be there is a case where
the information needs to be parsed properly.

Best,
Sebastien

[1] https://github.com/openmicroscopy/bioformats/blob/v5.1.10/components/formats-gpl/src/loci/formats/in/DeltavisionReader.java#L766
[2] https://github.com/openmicroscopy/bioformats/blob/v5.1.10/components/formats-gpl/src/loci/formats/in/DeltavisionReader.java#L1191

On 20 Jun 2016, at 21:07, Alexander Al Saroori <saroori.alexander at googlemail.com<mailto:saroori.alexander at googlemail.com>> wrote:


Hello again,

Sorry for emailing you again but I've just got the hint, that I should be more specific, since there are different DV files. That's why I tried all different DV data stacks I got so far from a OMX-V3 microsocope.

Retrieving the stage position from the meta data in Matlab works very good for (processed) data stacks using the provided software from Deltavision (Softworx). So I can get the information from reconstructed 3D SIM-stacks,  image stacks acquired in STORM mode(which are technically just single widefield images in a time series) and 3D deconvoluted stacks.

Unfortunately it does not work for  unprocessed SIM stacks, conventional 3D-stacks and which is why I am writing for data stacks with several time points and just one z-position. (experimental setup: 5000 images (every 10ms one image)). I know that the information of the stage position is stored in the data stacks since I can get the information using Softworx.

Working minimal code for 3D-Stack (several z-slices)

r= bfGetReader(fpath);
m = r.getMetadataStore();
m.getPlanePositionZ(0, 0)


ans = ome.units.quantity.Length: value[3612.2], unit[reference frame] stored as java.lang.Float


For the data stack with several time points, I just got

ans = []

Do I miss something, or is there any other commando I could use to get this information from my data stack?

Thank you very much!

Cheers,

Alex


On 20/06/16 19:33, Alexander Al Saroori wrote:

Hi together,

I have some problems to get the camera position stored in the metadata of my deltavision (DV) files, using Bio-Formats in Matlab. It works very good for single image stacks (with several z-slices) but not for data stacks with several timepoints and just one z-position. (experimental setup: 5000 images (every 10ms one image)). I know that the information of the camera position is stored in the time series since I can get the information using Softworx (provided Deltavision software).

Working minimal code for 3D-Stack (several z-slices)

r= bfGetReader(fpath);
m = r.getMetadataStore();
m.getPlanePositionZ(0, 0)


ans = ome.units.quantity.Length: value[3612.2], unit[reference frame] stored as java.lang.Float


For the data stack with several timepoints, I just got

ans = []

Do I miss something, or is there any other commando I could use to get this information from my data stack?

Thank you very much!

Cheers,

Alex


_______________________________________________
ome-users mailing list
ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users


The University of Dundee is a registered Scottish Charity, No: SC015096
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20160621/aa6beaaf/attachment.html>