FluoEM is a set of experimental and computational methods allowing to directly match fluorescently labelled axons to their 3D EM counterparts without label conversion. We provide the FluoEM code via a gitlab repository repository on gitlab released under the MIT license.
All 3D image data shown in the FluoEM paper can be accessed via our webKnossos demo server. WebKnossos is an efficient in-browser annotation tool for 3D image data accelerating neurite reconstruction for connectomics: Boergens, K.M., Berning, M., Bocklisch, T., Bräunlein, D., Drawitsch, F., Frohnhofen, J., Herold, T., Otto, P., Rzepka, N., Werkmeister, T., et al. (2017). webKnossos: efficient online 3D data annotation for connectomics. Nature Methods 14, 691.
The FluoEM paper was published in eLife:
Drawitsch, F., Karimi, A., Boergens, K.M., and Helmstaedter, M. (2018). FluoEM, virtual labeling of axons in 3-dimensional electron microscopy data for long-range connectomics. Elife 7. (doi:10.7554/eLife.38976).
An earlier version was posted at biorxiv on June 7, 2018. (doi: 10.1101/340802)
FluoEM was developed at the Max Planck Institutes of Neurobiology (2014) and Brain Research (2014 onwards). It is maintained by the Connectomics department at the Max Planck Institute for Brain Research, Frankfurt. All research was funded by the Max Planck Society.