OT2 arrived, requires setup to point of remote access color matching

[sgbaird]

[sgbaird]

Starting point: https://support.opentrons.com/s/ot-2/get-started-guide

[sgbaird]

[Neil-YL]

OT2 device is now connected to the AC-IoT network. Pipette is required to run the calibration.

[sgbaird]

P300 to be picked up tomorrow from organic chemistry lab

[Neil-YL]

P300 Single channel pipette was mounted on the right mount and calibrations were carried out for the deck, the pipette offset and the tip length with 300 µL Tip Rack. Attached is the calibration data JSON file.

opentrons-OT2CEP20240218R04-calibration.json

[Neil-YL]

SSH access for OT-2 (initial SSH set up for new keygen) https://support.opentrons.com/s/article/Setting-up-SSH-access-to-your-OT-2 Note: To generate RSA2048 key as shown in the support article:

ssh-keygen -t rsa -b 2048 -f ot2_ssh_key

USB connection is required to install the key pair to OT-2. I installed my key pair on the device and the key pair file on the PC side can be shared to other computers to establish the SSH connection in the future.

Connecting OT-2 with SSH https://support.opentrons.com/s/article/Connecting-to-your-OT-2-with-SSH

OT-2 have a built-in camera(resolution of 640x480px for still images and 320x240px for video): https://support.opentrons.com/s/article/Using-the-OT-2-s-camera

[sgbaird]

Awesome! Like we talked about, it would be nice to know what can be run directly on the OT-2 vs. what needs to happen through the GUI / PC side. Ideally, we'd be able to have an arbitrary Python file running on the OT-2 (i.e., the one that exposes remote access).

[Neil-YL]

I have written a protocol file matching our lab-ware and setup and successfully have two trial runs via the PC app and via the Jupyter Notebook on the web browser. (syntax is a little bit different)

To run it directly on OT-2, I think this documentation may be helpful, https://support.opentrons.com/s/article/Integrating-the-OT-2-with-other-lab-equipment I would look it up and have some trial lately.

[sgbaird]

Awesome! When you get a chance, do you mind taking a short video?

[Neil-YL]

Here is a video of a trial run via Jupyter Notebook (Pick up tip, move liquid from A1 to B1, drop tip)

https://github.com/user-attachments/assets/b1995e20-23bb-4595-b11d-8bc507aa9187

[Neil-YL]

I have successfully run a python code on the OT-2 via SSH with: opentrons_execute /path/protocol.py

but the robot ran without loading the calibration file, perhaps some initialising codes should be added prior to the run() code.

Though the documentation recommends install PyVisa to establish connection between devices, I think we can retain our practice on other devices (MQTT) without PyVisa since OT-2 is based on Raspberry Pi:

The core of the OT-2 is a Raspberry Pi 3+ running a custom Linux distribution.

[Neil-YL]

Received a software update this afternoon, the tip-pick-up location storage issue I mentioned in the morning seems to be resolved (at least I cannot reproduce it so far)

As for the "Failed to initialize" warning, according to this support article, it could be safely ignored: https://support.opentrons.com/s/article/Common-errors-when-running-opentrons-execute

deck_calibration and robot_settings not being found This is normal when executing a protocol and can be safely ignored:

[Neil-YL]

Have some ideas for the color sensor setup:

• Design a custom housing for the sensor and control board, matching the size of Opentrons labware. The control board will be positioned underneath the support/housing. Additionally, integrate custom labware into the OT-2 system to avoid collisions with moving tips. (This can likely be done by setting up a block with a specific height.)

• The color sensor can be picked up and moved to different slots (1, 2, 3) if it’s out of range.（the range of the color sensor needs to be tested first)

• The sensor labware can be easily relocated if the labware arrangement changes in the future, as the housing is designed to match the size of standard labware. Some sketching help to understand

  

• Power could be supplied via a battery (either integrated with the same labware or standalone) or through other potential wireless charging solutions. One quick idea is to charge the battery when the tip moves to the idle position (top-right corner).(should we determine the power consumption when designing the power supply? I saw one post discussing the power consumption of PicoW says ‘reading 4.6V, 52 mA using wifi and the LED, starting up it did spike up to ~150 mA’)

We can discuss together later to see if any new ideas come up.

[sgbaird]

Nice! Looking forward to chatting. I'm somewhat leaning towards a 6-point kinematic coupling similar to what's done for Science Jubilee (except all 3D printed) for the pickup.

[Neil-YL]

[sgbaird]

For the most part, we've moved our discussion to the other issue about the color sensor tool.

Simultaneous to this, Jackie from Alan's group plans to try out some things with Prefect and the OT-2.

[Neil-YL]

A demo run of 1 color measurement and 1dispense cycle:

https://github.com/user-attachments/assets/65ea91c4-4bda-48e4-9894-d84f507308ca

[Neil-YL]

A demo run of 3 dispense and 1 color measurement cycle:

https://github.com/user-attachments/assets/25ab0145-1de1-4ce0-91ab-ca743be11aa6

another POV:

https://github.com/user-attachments/assets/b7cc7935-3a14-446f-a01d-d79129bf3c28

[Neil-YL]

With RYB colors water:

https://github.com/user-attachments/assets/92a1e66f-6047-4ec4-8e00-3254414f7d0d

Noticing remaining liquid in tip after dispensing and droplets on the OT-2 deck, a blow-out process for the tip may be required during the procedure

[Neil-YL]

Added a blow-out step to a waste vial before returning the tip, with 25% speed control when moving to the waste vial. It takes around 2 mins to finish one cycle (1st pick up red tip: 0:05 and 2nd: 2:06)

https://github.com/user-attachments/assets/5496f83b-298b-46e8-9eb2-f117069cfed5

https://github.com/user-attachments/assets/c3e9a3e0-6de0-4824-8d7d-e7363f83deca