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autoliftout is a python package for automated liftout of cryo-lamella

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Automated cryo-liftout for electron microscopy

liftout is a python package for automated liftout for cryo-lamella preparation.

Getting Started

For detailed instructions on getting started, please see the Getting Started.

User Guide

For detailed instructions on how to use the program, please see the User Guide.

Quick Start

Installation

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 .

Install OpenFIBSEM dependency

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.

Preparation

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.

Running the Program

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.

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autoliftout is a python package for automated liftout of cryo-lamella

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