Blendervideo.avi video guides you through the full Serial Block Face EM dataset in the 3 orthogonal anisotropic planes meshed with the 3D model of few selected objects (microglia cell body-dark grey, nucleus- blue, mitochondria- orange and lyso-phagosomes- purple).

Segmented.blend is a Blender project of the segmented microglia. The file can be opened upon download and installation of  Blender (https://www.blender.org/). Once installed with the plugin NeuroMorph_3D_Drawing.py, the user will be able to navigate the 3D model, with the raw EM slices registered to the model. It is advised to follow a basic commands and navigation tutorial, that can be found anywhere online. The same project was used to generate the video of the repository. For more functionalities, the whole NeuroMorph add-ons suite can be installed (https://github.com/NeuroMorph-EPFL/NeuroMorph/wiki/3D-Drawing). A computer with a good amount of memory (at least 16GB) and a graphic card is highly recommended.

Generate_3D_image_stacks.ijm is a macro for imageJ to generate folders containing EM images in X,Y, and Z orientations, which are needed to visualise the slices within Blender with the given Segmented.blend file.
To use it, open the files dataset1.tif and dataset2.tif in imageJ. Run this macro (e.g. Plugins>Macro>Run). When asked, select the folder where the Segmented.blend file is stored. 
THIS OPERATION WILL TAKE APPROXIMATELY 18GB OF STORAGE.

Segmented.obj file contains all 3D objects segmented. Individual branches and filopodia can be idientified in the files as opened mesh (for surface measurement) and as closed mesh (for volume measurements).
Any 3D viewer should support this format. However this file contains a lot of object and can be hard to handle. 
We recommend to open this file with Blender (https://www.blender.org/), or instead open the .blend project with Blender that already contain all the meshes.