The Squid Control software is a Python package that provides a simple interface to control the Squid microscope. The software is designed to be used with the Squid microscope (made by Cephla Inc.).
See the installation guide for instructions on how to install and use the software.
To run the software, use the following command:
python -m squid_control --config HCS_v2
If you want to use a different configuration file, you can specify the path to the configuration file:
python -m squid_control --config /home/user/configuration_HCS_v2.ini
To start simulation mode, use the following command:
python -m squid_control --config HCS_v2 --simulation
To load a custom multipoint function:
python -m squid_control --config HCS_v2 --simulation --multipoint-function=./my_multipoint_custom_script_entry.py:multipoint_custom_script_entry
The Squid Control software now supports integration with Hypha, a generative AI-powered application framework designed for large-scale data management, AI model serving, and real-time communication. This feature allows users to register a Hypha service and a chatbot service for the microscope, enabling advanced automation and real-time collaboration.
Hypha is a framework that connects various computational and user interface components through Hypha-RPC, a bidirectional remote procedure call system. It supports real-time communication, scalable data management, and integration with AI models and tools. For more details, see the Hypha documentation.
To register a Hypha service for the microscope, follow these steps:
- Follow the Hypha Tutorial: Refer to the Hypha tutorial for detailed instructions on setting up the service.
- Run the Hypha Service Script: After completing the setup, start the Hypha service by running the following command:
python start_hypha_service.py
This script will initialize the Hypha service for the microscope.
You can read the tutorial at Hypha Tutorial to learn how to use the Hypha service for microscope control.
Cephla Inc.
The current branch is a frok from https://github.com/hongquanli/octopi-research/ at the following commit:
commit dbb49fc314d82d8099d5e509c0e1ad9a919245c9 (HEAD -> master, origin/master, origin/HEAD)
Author: Hongquan Li <hqlisu@gmail.com>
Date: Thu Apr 4 18:07:51 2024 -0700
add laser af characterization mode for saving images from laser af camera
How to make pypi work:
- Register on pypi.org
- Create a new token in the account settings
- In the repository setting, create a new secret called
PYPI_API_TOKENand paste the token in the value field - Then, if you want to manually publish a new pypi package, go to actions, select the
Publish to PyPiworkflow, and click onRun workflow.