liftout
is a python package for automated liftout for cryo-lamella preparation.
For detailed instructions on getting started, please see the Getting Started.
For detailed instructions on how to use the program, please see the User Guide.
Clone this repository:
git clone https://github.com/DeMarcoLab/autoliftout.git
Install dependencies and package
cd autoliftout
conda env create -f environment.yml
conda activate autoliftout
pip install -e .
Follow the instructions in OpenFIBSEM to install the fibsem dependencies.
ThermoFisher Microscope Load Application Files
- Load the application files, autolamella.xml, and cryo_Pt_dep.xml into XtUI following the manufacturer instructions.
- These application files are used for milling and platinum deposition respectively. To provide your own, please edit the system.yaml file.
System File (system.yaml)
- Edit the system.yaml file to match your system configuration
Protocol File (protocol.yaml)
- Edit the protocol.yaml file to match your desired protocol
Preparing the Needle
- Mill the end of your manipulator so there is a 10um flat surface. TODO: image
Preparing the State
- Save the lamella and landing states (Raw coordinates) in the protocol.yaml file.
- These are the initial positions for selecting lamella and landing positions.
Once you have installed all the dependencies and completed the preparation steps, run:
conda activate autoliftout
autoliftout_ui
The AutoLiftout User Interface should appear on the screen, ready to start.