oOo is a High-Performance Parallel Magnetic Tweezer program for real-time monitoring of protein folding and unfolding under force.
- Windows
- Ximea camera (xiQ USB 3.0 SuperSpeed)
- Piezo Controller (P-725.xDDPIFOC adnd PI-E-709) ( We tested on AMD threadripper Pro 3975wx 32 core 3.5Ghz 64GB RAM 64Bit Windows 10 Pro 20H2 )
To get started with this project, you'll need to have Python 3.8 and its dependencies installed on your machine. Here's how you can do it:
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Python 3.8: Visit the official Python website at python.org and download the Python 3.8 installer for your operating system.
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Ximea Drivers : Visit Ximea and install the camera drivers then install the xiAPI. ( We have used https://www.ximea.com/support/attachments/37/XIMEA_API_Installer.exe with all API option ticked while installing and the used this guide to install ximea python API https://www.ximea.com/support/wiki/apis/Python_inst_win )
python camtest.py
if this return no error we good to go!
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Dependencies: Once Python 3.8 is installed, open a terminal or command prompt and run the following command to install the required dependencies:
pip install -r requirements.txt
This command will install all the necessary dependencies listed in the
requirements.txtfile.
To run the program, use the following command:
python oOo.py [arg1] [arg2]Usage: [arg1] can be
fresh -> To take fresh stack.
start -> Start data aquisition.
plot -> Plot the collected data with [arg2] as bead number.
stackplot -> Plot stack graph.
You can modify specific settings in the config.py the default settings are:
stack_size = 200 # Size of the stack
exposure = 1000 # Exposure time in milliseconds
resolution = 256 # Resolution of the image
workers = 20 # Number of workers for processing
driftworkers = 2 # Number of workers for drift correction
qu_limit = 100 # Queue limit for processing
driftworker = 4 # Number of workers for drift calculation