FluoEM is a set of experimental and computational methods allowing to directly match fluorescently labelled axons to their 3D EM counterparts without label conversion.

The FluoEM code package is written in Matlab and does not require any additional toolboxes, other than the core matlab libraries.

It allows to:

• Efficiently handle and register correlated 3D graph representations of neurites
• Identify potential neurite correspondences based on structural divergence

It was developed at the Max Planck Institute of Neurobiology (2013 - 2014) and the Max Planck Institute for Brain Research (2014 - 2018)

If you have git installed, you can clone the FluoEM repository by entering

$ git clone https://gitlab.mpcdf.mpg.de/connectomics/FluoEM.git

into your terminal.

Alternatively, you can download the code as a compressed file via the gitlab frontend (click the small cloud icon).

The FluoEM code package is written in Matlab, so you will need Matlab license to run it. You do not need any additional Matlab toolboxes on top of that, the matlab core libraries are sufficient.

After cloning or downloading the code, navigate into the FluoEM main directory inside Matlab and execute

>> setup()

inside the Matlab command window to set the required paths. After this, you are ready to go.

The FluoEM package was developed by

• Florian Drawitsch

under scientific supervision by

• Moritz Helmstaedter

Some of FluoEM's functionality is built around webKnossos (.nml) neurite skeleton files and makes use of an efficient .nml parser developed by

• Alessandro Motta

The Matlab class used to represent single neurite skeletons was developed by

• Benedikt Staffler
• Alessandro Motta
• Florian Drawitsch
• Ali Karimi
• Kevin Boergens

This project is licensed under the MIT License - see the LICENSE.md file for details

We thank

• Matt Jacobson for providing the “Absolute Orientation – Horn’s method” Matlab central package we used in our affine registration workflow and
• Dirk-Jan Kroon for providing the “B-spline Grid, image and point registration” Matlab central package we used for our free-form registration workflow