Run the following script in terminal to clone the repo and set up the environment
wget https://raw.githubusercontent.com/hongquanli/octopi-research/master/software/setup_22.04.sh
chmod +x setup_22.04.sh
./setup_22.04.sh
Reboot the computer to finish the installation.
image stitching dependencies (optional)
For optional image stitching using ImageJ, additionally run the following: ``` sudo apt-get update sudo apt-get install openjdk-11-jdk sudo apt-get install maven pip3 install pyimagej pip3 instlal scyjava pip3 install tifffile pip3 install imagecodecs ```Then, add the following line to the top of /etc/environment (needs to be edited with sudo [your text editor]):
JAVA_HOME=/usr/lib/jvm/default-java
Then, add the following lines to the top of ~/.bashrc (or whichever file your terminal sources upon startup):
source /etc/environment
export JAVA_HOME = $JAVA_HOME
export PATH=$JAVA_HOME/bin:$PATH
Installing drivers and libraries for FLIR camera support
Go to FLIR's page for downloading their Spinnaker SDK (https://www.flir.com/support/products/spinnaker-sdk/) and register.Open the software/drivers and libraries/flir folder in terminal and run the following
sh ./install_spinnaker.sh
sh ./install_PySpin.sh
Add udev rules for ToupTek cameras
sudo cp drivers\ and\ libraries/toupcam/linux/udev/99-toupcam.rules /etc/udev/rules.d
Copy the .ini file associated with the microscope configuration to the software folder. Make modifications as needed (e.g. camera_type, support_laser_autofocus,focus_camera_exposure_time_ms)
python3 main_hcs.py
To start the program when no hardware is connected, use
python3 main_hcs.py --simulation
To install the development environment, run the following script in terminal
conda create -n squid-control python=3.10 -y
conda activate squid-control
pip install -r requirements.txt
pip install -e ".[all]"