preprocessing_arrenberg_practical_2023

authors: Yue Zhang, David Burkhardt, Tim Hladnik (AG Arrenberg, CIN, Tuebingen University)

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Installation of Anaconda and virtual environment:

1. Install an Anaconda distribution of Python (https://www.anaconda.com/products/distribution) -- Choose Python 3.x and your operating system.
2. Download the repository and extract all files into your target directory
3. Open an anaconda prompt / command prompt with conda for python 3 in the path
4. Change directory to where the environment.yml is and run conda env create -f environment.yml
5. Open the Anaconda Navigator and change the environment to ca_prepro_arrenberg
6. Install and launch Jupyer Notebook (using the Anaconda Navigator) and open the analysis scripts

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Usefull Links (MView for viewing .MDF files and HDFView for viewing .hdf5 files):

• https://www.sutter.com/SOFTWARE/microscope_frame.html
• https://www.hdfgroup.org/downloads/hdfview/