Happy to see this project taking some momentum.
Technically I am sure @kaspar you can do it. I have made a working prototype of a software in PureData . I know how to control all the elements in the machine (lasers, filter motors, x/y motors etc). For the scanning I know the commands to trigger scanning in the FPGA and I can take pictures with the Hamamatsu TDI demo program. ( documented here: https://www.hackteria.org/wiki/HiSeq2000_-_Next_Level_Hacking , maybe some things need to me explained more, I am happy to do that).
So what would needs to be done:
Better graphical interface. With some sliders, knobs, speed settings, preview window, maybe selecting scanning area by mouse, choosing the camera and filters etc.
Opening 6 serial ports (for the different units) and sending the corresponding commands. The commands are text based (see command list on the wiki) and as easy as “LASER ON” “LASER OFF”.
Reading the picture form the frame grabber. I now do this with the Hamamatsu TDI demo software. It works. However I think it would be a big improvement to integrate this with the control software. The pictures could be previewed in the interface. Automatic scanning etc would be possible. For this we would need to interface with the framgrabber via the DCAM Interface Library. The library is openly available from Hamamatsu and probably well documented.
Post processing of some (BIG) images. This is kind of optional as it can be done in ImageJ. Would be nice to stitch scanned lines together into one big picture automatically. Probably more a question on how to program it properly and the power of your computer.
Extra features: Once the basic software is running there are - as always - endless improvements that could be made, such as auto-focusing, combining fluorescent images with bright light etc etc.
Integration into Micromanager sound interesting if possible with the machine we have. (As I said earlier the TDI scanning must be solved as it is probably not standard in this software). Also we have to consider what is easier (stand alone or integration) and flexibility for other uses - I can still imagine to do some sequencing with the open software (by integrating the flushing of the chips with the chemicals between images, so would need to control some valves and pumps) - or also turn the machine into a flow cytometer…
For the WeMakeIt campaign, I also think it might be an easy way to get some extra money. Need to setup a description and a video - probably us talking something and some images from the prototype. Then administratively its very lean, you basically just get the money. Maybe we need to think of a simple use case to include in the campaign. Such as finding micro-plastic in soil (what we allready tried). We can then spread the word and hopefully find some more people that have a HiSeq and want to reuse it. (And yes, GaudiLabs would just be a gold sponsor of the project).
** Have to check, I think this science booster ends soon, maybe already end of this year. So let’s do in now**
For working on the machine. Ask around, these machines are available at sequencing labs and universities, so if you could get one @kaspar that would be fun. Probably the crowd-funding campaign would even help getting more machines if we mention that we need some for you. (Institutions payed millions for these machines only some years ago and they are sad to see them be without use alread.y)
Then it would probably be good if you could come to GaudiLabs, @kaspar and @jmarkham so that I can show you the scanning and transfer as much knowledge from my hack to you. Between Chrismas and NewYear would be good for me (I will skip CCC or maybe we can even meet there). Best if we already have to money by then.