Dictyviz

This repository provides a set of tools to generate orthogonal maximum intensity projections, movies from 4D zarr imaging datasets, and perform 3D optical flow analysis using a dedicated submodule.

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Getting Started

1. Clone the dictyviz repo

After cloning the repository, download the contents of the submodule:

git submodule update --init --recursive

2. Install the dictyviz environment

conda env create -f environment.yml
conda activate dictyviz

3. Install the optical3dflow environment

The 3D optical flow analysis relies on a separate environment with additional dependencies located inside the submodule. To install it, first ensure you have the submodule content downloaded (see step 1).

conda env create -f optical3dflow_environment.yml
conda activate optical3dflow

4. Running scripts

To run scripts, navigate to the right directory and run the correct bash script. Note: to run anything that requires opticalflow (2d or 3d), the optical3dflow environment must be activated. For everything else, the dictyviz environment should be activated.