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

[Alexander Al Saroori]

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
>
>

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