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DarEM

Installation

Note: the last supported python version is 3.9 as Tensorflow 2.5.1 is not available on later python versions

Linux

Install the following prerequisites

  • CUDA Toolkit 11
    • Required for training or fast prediction on a GPU. Not necessary for slow prediction on a CPU
  • conda
    • can be installed through anaconda/miniconda or miniforge
    • Using other ways to create virtual python environments is possible, but our installation instructions are based on conda
  • gcc
    • Run sudo apt install gcc in a terminal
  • Protobuf V3.19
  • git
    • Run sudo apt install git in a terminal

Open a terminal and run

conda create -n DarEM python==3.9 cudnn=8.2
conda activate DarEM
git clone https://github.com/tensorflow/models.git
cd models/research
git checkout 457bcb8595903331932e2faf95bec8ba69e04688
protoc object_detection/protos/*.proto --python_out=.
cp object_detection/packages/tf2/setup.py .
pip install .
cd ../../
git clone https://github.com/DavidKleindienst/DarEM
cd DarEM
pip install -r requirements.txt

To run DarEM run on python Train.py for training or python Predict.py for Prediction.

Windows

Ensure the following prerequisites are installed:

  • CUDA Toolkit 11
    • Required for training or fast prediction on a GPU. Not necessary for slow prediction on a CPU
  • conda
    • can be installed through anaconda/miniconda or miniforge
    • Using other ways to create virtual python environments is possible, but our installation instructions are based on conda/miniforge
  • Protobuf V3.19
    • Download protoc-3.19.4-win64.zip on 64-bit Windows or protoc-3.19.4-win32.zip on 32-bit Windows
    • Unzip the downloaded file and add the path to /bin to your PATH environment variable
  • Visual Studio Build Tools
    • In the installer, select "Desktop Development with C++".
    • A reboot may be required
  • Git

Ensure that the conda command is available in powershell If not open Anaconda prompt and run conda init powershell, then open a new powershell. If conda is still not available, you need to allow execution of powershell scripts. Open an adminstrator powershell and run Set-ExecutionPolicy RemoteSigned. After you open a new powershell, the conda command should now be available

Open a new powershell and run

conda create -n DarEM python==3.9 cudnn=8.2
conda activate DarEM
git clone https://github.com/tensorflow/models.git
cd models/research
git checkout 457bcb8595903331932e2faf95bec8ba69e04688
protoc object_detection/protos/*.proto --python_out=.
cp object_detection/packages/tf2/setup.py .
pip install .
cd ../../
git clone https://github.com/DavidKleindienst/DarEM
cd DarEM
pip install -r requirements.txt

To run DarEM doubleclick on Train.cmd for training or Predict.cmd for Prediction.

Setting up the scripts for automatic image acquisition with SerialEM

Copy the contents of the SerialEMImageAcquisitionScripts folder to a convenient location on your microscope PC and ensure pyEM is installed. You will need to modify the following setting in the Acquire_Tilt_Series.txt script dependent on your desired imaging parameters:

  • hm_mag
    • the magnification at which the tilt series will be taken
  • hm_C2
    • the intensity (C2) setting at which the tilt series will be taken
  • tilt_delay
    • the time (in ms) to wait after a tilt for stabilization before starting the acquisition
  • offset
    • the defocus at which the eucentric focus is reached, see the comments in the scripts for how to measure this value
    • the correctness of this value should be checked occasionally (especially if you encounter unfocused images) and updated if necessary
  • tilt_angles
    • A list of tilt angles at which the images should be taken
    • The default is -24.5, -12.2, 0, 12.2, 24.5
    • Ensure to not take more extreme angles than your microscope setup permits

Weights for PSD detection

We've made the weights we trained for PSD detection available. If you would like to use them either to directly for finding PSDs or as starting point for additional training, please download them here and place them in the appropriate folder under DarEM/models/

Usage

These are some quick instructions including screenshots of relevant settings. Please refer to our book chapter linked below for further details and explanations.

Acquiring a map

Use File -> New Montage... to acquire an overview image of the whole replica. Example setting that we've used:

You should obtain an overview image of your replica such as this.

Open the navigator panel with Navigator -> Open. Your overview image should alread be contained in the list. If not, make sure the low mag image was saved in a file and open in SerialEM, and click on the "New Map" button in the Navigator panel. Click add points and add a point on an easily recognizable structure (we usually use folds or holes of the replica). Find the same structure at the resolution that you would like to use to search for your profiles of interest and click on it to add the green marker. Then apply Navigator -> Shift to Marker (select All items at the registration of the image with m in the dialogue box) to register the shift in x/y coordinates between the resolution used on the overview image and the resolution used for acquiring the map.


Double-click on the low mag map taken previously from the Navigator list to reload it. Then, select add polygon in the navigator panel and draw a polygon around your area of interest. Save the navigator file (Navigator -> Save) in the same folder where you will save your images. Set up a polygon montage (Navigator -> Montaging & Grids -> Setup Polygon Montage) using setting similar to the following

When given the choice to make a map from the montage, answer Yes. The montage will now be taken, which may take a while. If you perform the profile detection on a different PC, you can run the profile detection in parallel to the image acquisition (be sure to save your images to a folder that you can access from both PCs in this case). Otherwise (you intend to use your camera PC for profile detection), please wait for the acquisition to finish before you proceed.

Automatically detecting profiles of interest

When running profile detection from the camera PC, you should be able to select the script for profile detection in the tools window. Running it will open a window where you specify the network you would like to use for the prediction (e.g. you may have different trained networks for detecting different kinds of profiles). The location of your files will be automatically passed to the script.

When running it on a different PC please open the Prediction Menu and select the appripriate .nav file and the network you would like to use. This prediction can run in parallel to the imaging and will wait for new images to be saved when necessary.

Acquiring tilt series of the profiles of interest

Use the coords2pts.py script to generate a new .nav file (will be called [your_nav_file_name]_with_points.nav). Close the current file with File->Close then use Navigator->Read & Open... to read the newly generated navigator file.

You should now see your map with points annotating the found profiles

You can zoom in to verify that the detections correspond to profiles of interest

Open Navigator -> Acquire at Items to start the tilt_series of all selected points using the Acquire_Tilt_Series.txt script

Training DarEM for deteting relevant profiles

Please acquire low-res maps as described above, which will serve as training images. Please refer to our boock chapter linked below for instructions on how to annotate the images and train the deep neural network.

Citation

If you've used this software for your research, please cite

Kleindienst, D., Costanzo, T., Shigemoto, R. (2024). Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning. In: Lübke, J.H., Rollenhagen, A. (eds) New Aspects in Analyzing the Synaptic Organization of the Brain. Neuromethods, vol 212. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-4019-7_8