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

[Alexander Al Saroori]

Hi Sebastien,

Thank you very much for your reply!

Your point was very true, that the problem was the presence of the log 
file (which is probably somehow corrupted). After deleting the logfile 
it works perfectly.

Thanks again for your help!

Best,
Alex

On 21/06/16 13:17, Sebastien Besson (Staff) wrote:
> 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
>>>
>>>
>>
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