TrakEM2 to BigDataViewer

[Thomas]

Dear List,

is there an advised workflow to go from a large TrakEM2 project (many layers, many tiles per layer) to BigDataViewer ? 

Exporting each layer to file is an option but how to proceed with single layers larger than 2 gigapixels ? I can export subpatches from single layers in TrakEM but how to read them wit BigDataViewer ? Maybe I missed something in the API ?

Thanks for your help

Best regards

Thomas

[Thomas Templier]

Thank you Stephan, that looks exactly like what I wanted.
Best regards
Thomas


On 10/20/2015 8:38 PM, Saalfeld, Stephan wrote:
> Hi Thomas,
>
> I had that running in a branch some time ago but lost track of it
> because lack of interest and urge:
>
> https://github.com/bigdataviewer/bigdataviewer-core/tree/trakem2/src/main/java/bdv/img/trakem2
>
> will need some adjustment to the current API but should still work
> otherwise.
>
> This backend feeds BigDataViewer directly from the currently opened
> TrakEM2 project. It generates RGB pixel data including the overlays and
> segmentations that you have currently visible, i.e. everything that you
> see in the Display and that you would get by Export > Make flat image
>
> Best,
> Stephan

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