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CebraEM
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Volume SEM data segmentation
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# CebraEM ## Installation ### Support for Linux and Windows Note that CebraEM is developed on Linux. We have tested CebraEM on Windows and are currently working on a stable solution for Windows machines. Note that for Windows 10, a Windows Subsystem for Linux ([WSL](https://learn.microsoft.com/en-us/windows/wsl/about)) has to be installed for CebraEM to run. In Windows 11 this is already installed by default. ### Installation of the MoBIE browser Follow the instruction [here](https://github.com/mobie/mobie-viewer-fiji/) to install the Fiji and the MoBIE browser which includes these steps: - Download [Fiji](https://imagej.net/software/fiji/downloads) for your operating system - Unpack Fiji to any location on the filesystem - Open Fiji and install MoBIE: - Open the Fiji upater using ```Help -> Update...``` and wait for the updater to start up (may take a moment) - An information prompt will probably report that 'Your ImageJ is up to date!'. Press ```OK``` - In the "ImageJ Updater" window click ```Manage Update Sites``` - In the "Manage Update Sites" window scroll down or search for "MoBIE" and tick the box next to it - Press ```Apply and Close``` - Back in the "ImageJ Updater" window click ```Apply Changes``` which will now trigger download and installation of the required packages - Close and re-open Fiji to complete the installation TODO: Alternatively, can download and extract a Fiji that already includes MoBIE from [this release](https://github.com/jhennies/CebraEM/releases/download/v0.1.0/fiji-linux64-with-mobie.zip). After successful installation of MoBIE you can open a CebraEM/MoBIE project using ```Fiji -> Plugins -> MoBIE -> Open -> Open Collection Table...``` This will pop up a dialog where you need to specify the following: - For the field "Table Path", select the file ```mobie.csv``` from your project directory - Make sure "Data Root" is set to ```UseTableFolder``` - Make sure "Data Root Folder" is empty ### Download of the CebraEM source code Here, you have two options: #### 1. Download the source code in the [latest release](https://github.com/jhennies/CebraEM/archive/refs/tags/v0.0.3b.zip) - Now unpack the contents to some path of your choice (here I'm now assuming you created a folder called ```src``` in the user directory) - The path to CebraEM will now look something like this: ```~/src/CebraEM-v0.0.1/``` (Linux) or ```C:\Users\username\CebraEM-v0.0.1\``` (Windows) - Remember this path, this will be referred to below as ```/path/to/CebraEM``` ***OR*** #### 2. Clone the CebraEM repo into a path of your choice: ``` cd /path/to/ # !!Replace the folder name!! git clone https://github.com/jhennies/CebraEM.git ``` The path to CebraEM will be referred to below as ```/path/to/CebraEM``` ### Installation of Miniconda Install [miniconda](https://docs.anaconda.com/free/miniconda/) on your computer. I generally recommend using the mamba package for installing the conda environments. Open a terminal and install mamba into the base environment with: ``` conda install -c conda-forge mamba ``` For the following descriptions an installation of Mamba is assumed (otherwise just replace "mamba" -> "conda") ### CebraEM conda environment These commands install CebraEM as well as all dependencies except pytorch (run each of these lines in your terminal/prompt): ``` cd /path/to/CebraEM mamba env create -f environment.yaml conda activate cebra-em-env pip install -e ./cebra-em-core/ pip install -e ./cebra-ann/ pip install -e ./cebra-em/ ``` For pytorch you will need to determine your Cuda version and select the correct installation call. Please refer to https://pytorch.org/get-started/locally/ for further information. As an example, for our system with Cuda version 11, we installed pytorch successfully using this pip install command: ``` pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu118 ``` For Cuda version 12, this works for us: ``` pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu121 ``` **Now it is important to test the installation** The following script runs the main steps of the CebraEM pipeline using a small test dataset. ``` python test_installation.py ``` Possible errors: ``` ModuleNotFoundError: No module named 'torch' ``` The installation of pytorch is missing or did not work properly. Run ```nvidia-smi``` to determine your Cuda version and refer to https://pytorch.org/get-started/locally/ to determine the proper pytorch installation commands ## CebraEM [CebraEM readme](cebra-em/README.md) Contains: - Usage of CebraEM ## CebraANN [CebraANN readme](cebra-ann/README.md) Contains: - Specific installation for the cebra-ann package in case CebraANN needs to be run on a separate machine - Usage of CebraANN ## CebraNET [CebraNET readme](CebraNET_README.md)
