So things have not really worked out as hoped since the last update. We had a productive time commissioning @bengtsjolen’s machine in Berlin in January, but since then I’ve had other obligations and now COVID-19 has made it impossible to visit Berlin.
However I have been thinking about how to continue and especially how to accelerate development once I can access a HiSeq again.
Re-using OpenFlexure/LabThings
I’d like to change course and make sure to re-use and contribute back towards @kpandit 's python module. The main reason Micromanager is so appealing is that we get a GUI, features like auto-focus and scripting. Today my colleague here at the Uni of Bath gave a presentation about the work he’s been doing to generalise the Openflexure microscope client which made me think we should use a fork/adaptation of this as our GUI and high-level scripting interface.
It’s written in Python and VueJS/Javascript for the GUI. This is not only a tech stack that I feel I’ll be more productive with, it also makes sure we can integrate @kpandit’s work.
It definitely has less features and is less mature than Micromanager but on the other hand it’s much more adaptable and hackable.
See here to get an idea of what the client looks like:
The nascent standardisation effort around it is called Labthings:
Budget & aquiring a machine in the UK
I’ve updated the budget and we currently have CHF 5693.74 remaining. Since we haven’t been so lucky as to be donated a machine in the UK yet. I wanted to gauge people’s opinion on using around CHF 1300 or so to buy one. Here is a poll:
Buy a HiSeq for around CHF 1300 in the UK.
No, save the money and travel to Berlin when flights resume.
Hey! Just wanted to add that I am also stuck away from Berlin and the Hiseq(in Stockholm - frustrated by not being able to play around with the machine for quite some time now). Before I left Berlin last time I even sorted a bluetooth power switch for both me and Kaspar to be able to remotely power on and off the machine while not being on location, never got around to hooking it up though and didn’t expect not to be able to come back for such a long time. We’ll see how things go but as soon as borders open up we will go back to Berlin and stay for a couple of months at least and in the best of worlds that happens on the 15th of June unless Swedes are considered persona non grata for epidemiological reasons… Regardless more machines is better so if you find one for 1300 CHF I’d say go for it!
I agree with all that @kaspar. Given how far Kunal has got then arguably we should just contribute to that code base. I’m open to using open flexure if that’s going to be easier for you. It has the advantage of also being in python and if we can get the camera working under linux then the whole thing becomes much nicer. How does OF talk to pyseq? Looking here it seems like there needs to be the same sort of hardware abstraction and definition process as happens in MM. Happy to discuss if you want or to just leave it with you. Regarding a machine, how much would it cost to ship one from Germany? Just in case another free one is available.