[ome-users] .dv large time series file open bug?

[Sebastien Besson (Staff)]

Hi Dan,

Thanks for following up on this thread. Unfortunately we do not have any recent specification
file documenting this new Deltavision format. Without knowing the specifics, we implemented
a minimal workaround in Bio-Formats 5.2.3 released today [1] which should hopefully deliver
support for these large time-series files to the community, including your customers.

In the mid-term, updating the Bio-Formats reader to use the exact format specification is
certainly a more robust and maintainable approach as we have seen with other proprietary file
formats. In addition to the storage of the number of timepoints in the header, is there any other
major change in the specification that would affect Bio-Formats? Would you be allowed to share
part or all of this new Deltavision format specification?

Best,
Sébastien

[1] https://www.openmicroscopy.org/community/viewtopic.php?f=11&t=8133


On 5 Oct 2016, at 09:13, Daniel White <dan at chalkie.org.uk<mailto:dan at chalkie.org.uk>> wrote:

Hi Bio-formats  folks,

here is some more info about opening large time series .dv files, from the software engineers at the DeltaVision factory.
Does the latest .dv file format spec doc you have include the below info?
If not, let me know.

cheers

Dan


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There are two types of .dv formats: the old one, and the new one that we started using in 2006 which allows for much larger numbers of time-points.  From our software team, here’s the logic needed to determine the number of time-points in the file from the header of any .dv image file.  The complexity comes from backwards compatibility, but it should be straightforward enough!

determine the image file type by reading the 16-bit integer at header byte 160

if the image file type is >= 100 then
determine the number of time-points from the 32-bit integer at header byte 852

else if the image file type is < 100 then
determine the number of time-points from the 16-bit integer at header byte 180

If you could pass this along to the bioformats group, that would be great.

Let me know if you/they need any more information.

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