search

beniroquai / Opentrons-Microscope-Platereader

Other
18 stars 0 forks source link

Help Needed: Preinstalled image for OFM using a Nvidia Jetson Nano #19

Open jsmithe2 opened 4 months ago

jsmithe2 commented 4 months ago

Hello,

I am trying to emulate the exact UC2-Hi2 microscope you made to integrate into an opentrons system. I have purchased all the parts required for this and I am having trouble connecting them. I am using a Jetson Nano, a CMOS camera and and a Neje master 2 mini. You posted a warning in the README section of the Hi2 repository that looks like this:

_**"Warning: This is still under strong development. We derived the software to control the GRBL-based XYZt stage from the Openflexure microscope project by Bowman et al. Instead of using a Raspberry Pi camera, we use an Nvidia Jetson Nano singleboard computer and run a customized version of the OFM server that can control the GRBL board and the monochrome CMOS camera.

A detailed set of instructions for installing the Openflexure Server (OFM Server) can be found in a dedicated README_SOFTWARE.md (it is under construction..). In case you want a preinstalled image, please contact us!"**_

Is there a preinstalled image for a custom OFM server preinstalled image that would work best for this? Is this posted anywhere? This warning makes me skeptical that I'll be able to get this to work now that I have collected all of the necessary parts.

jsmithe2 commented 4 months ago

Is the correct image included in the paper "An Open-Source Modular Framework for Automated Pipetting and Imaging Applications"? There was a Zenodo link with a file named '[2021_06_23-NVIDIA_JETSON_IMAGE_OFM_IMJOY_64GB.rar]'. Is the correct one to install on the Jetson Nano?

beniroquai commented 4 months ago

Hey @jsmithe2, sorry for my late reply (also on the other github issue I saw). I must admit that this project is already fairly old and I am working on an updated version, which using a different software. It's called ImSwitch and can also run on the Jetson. I have gained a lot of experiences, both in hard- and software and improved it quiet a lot. We don't use the openflexure software anymore. I think it would not be too difficult to add a stage controller for the Neje stage to ImSwitch. Are you familiar with python programming? the software I'm talking about can be found here: https://github.com/openUC2/ImSwitch/ including an installation tutorial for the jetson.

jsmithe2 commented 4 months ago

@beniroquai Thanks for the reply. I am just a beginner at python coding as I am mostly an analytical chemist. I am trying to automate my work in the opentrons OT2 and requires a microscope. The one in the paper is perfect for what I need. I have almost all the parts currently so I am going to get it to work no matter what. I would like to use your imswitch software. Is the neje laser stage the only thing that is not currently compatible with imswitch from the Hi2 module? Do you have some recommendations on how to add the stage controller to this software? Also, can the opentrons jupyter notebook be connected with the imswitch software like you showed with the openflexure software?

beniroquai commented 4 months ago

So what you could do is using the CNC board with the ESP32 arduino-like board (forgot the correct name, has an Arduino UNO footprint) and flash our firmware https://openuc2.github.io/docs/Investigator/STORM/Electronics/#flashing-the-firmware This directly integrates with the UC2-REST and ImSwitch. ImSwitch runs on your computer (Installer) and we could integrate the HTTP interface from the opentrons there. Makes sense?