TrakEM2 to BigDataViewer

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

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

--
--
Please avoid top-posting, and please make sure to reply-to-all!
 
Mailing list web interface: http://groups.google.com/group/fiji-devel

---
You received this message because you are subscribed to the Google Groups "Fiji-devel" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
For more options, visit https://groups.google.com/d/optout.
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: TrakEM2 to BigDataViewer

Thomas
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
>
> On Fri, 2015-10-09 at 18:58 -0700, Thomas wrote:
>> 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
>> --
>> --
>> Please avoid top-posting, and please make sure to reply-to-all!
>>  
>> Mailing list web interface: http://groups.google.com/group/fiji-devel
>>
>> ---
>> You received this message because you are subscribed to the Google
>> Groups "Fiji-devel" group.
>> To unsubscribe from this group and stop receiving emails from it, send
>> an email to [hidden email].
>> For more options, visit https://groups.google.com/d/optout.

--
--
Please avoid top-posting, and please make sure to reply-to-all!

Mailing list web interface: http://groups.google.com/group/fiji-devel

---
You received this message because you are subscribed to the Google Groups "Fiji-devel" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
For more options, visit https://groups.google.com/d/optout.
Loading...