HamanatsuHam TDI support for HiSeq

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HamanatsuHam TDI support for HiSeq

John Markham

Hi, I was wondering if the HamamatsuHam adapter supports time delay integration (TDI). I see no mention of it so I am presuming not - but since the code is unavailable it's a bit hard to tell. TDI is used in the old HiSeq sequencers which have a S10405 line-scanning CCD chip with a C10000-509 control board and a phoenix frame grabber. There are thousands of HiSeqs out there and at the end of service they can be potentially be repurposed (as has been done with the older Illumina instruments). I have downloaded the dcam-api and it looks like it there is everything needed to make the camera work. It needs to have the interface done connecting the relevant calls to the device adapter class in micro-manager. There will likely need to be some other hacking done to synchronise it properly with the stage. I and others (https://forum.hackteria.org/t/hiseq2000-next-level-hacking/325/40) would be happy to do that. Is it possible to get access to the source for the existing HamamatsuHam device adapter? That would make our job much easier. We would be happy to make whatever we do available for others to use.

Regards,

John



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Re: HamanatsuHam TDI support for HiSeq

Stuurman, Nico
Hi John,

That sounds like a fun plan, and I'd love to see it come to fruition.  Regretfully, Hamamatsu does not want us to make the source code to their adapter (which they write themselves) available.  The best option is to contact Hamamatsu and ask them if they can share the source code with you (and - preferably - review your code changes and push them back into the MM source code repository).

Good luck!

Best,

Nico

On 11/18/2018 3:27 PM, John Markham wrote:
Hi, I was wondering if the HamamatsuHam adapter supports time delay integration (TDI). I see no mention of it so I am presuming not - but since the code is unavailable it's a bit hard to tell. TDI is used in the old HiSeq sequencers which have a S10405 line-scanning CCD chip with a C10000-509 control board and a phoenix frame grabber. There are thousands of HiSeqs out there and at the end of service they can be potentially be repurposed (as has been done with the older Illumina instruments). I have downloaded the dcam-api and it looks like it there is everything needed to make the camera work. It needs to have the interface done connecting the relevant calls to the device adapter class in micro-manager. There will likely need to be some other hacking done to synchronise it properly with the stage. I and others (https://forum.hackteria.org/t/hiseq2000-next-level-hacking/325/40) would be happy to do that. Is it possible to get access to the source for the existing HamamatsuHam device adapter? That would make our job much easier. We would be happy to make whatever we do available for others to use.

Regards,

John



_______________________________________________

The information in this email is confidential and intended solely for the addressee.
You must not disclose, forward, print or use it without the permission of the sender.

The Walter and Eliza Hall Institute acknowledges the Wurundjeri people of the Kulin
Nation as the traditional owners of the land where our campuses are located and
the continuing connection to country and community.
_______________________________________________





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