Connectomics

Scanning electron microscopy (SEM) provides the superb resolution required to visualize neuron connections. 3D ultra-resolution imaging can be achieved with serial block face imaging using the ZEISS GeminiSEM or ZEISS Sigma family of electron microscopes integrated with 3View. Or FIB-SEM tomography can be used for 3D visualization of neurons using ZEISS Crossbeam.

ZEISS has developed a novel multi-beam SEM technology for imaging large sample areas, the ZEISS MultiSEM family. In partnership with the automated tape collecting ultramicrotome, which cuts the sample into ultrathin sections, MultiSEM dramatically speeds up the acquisition of 3D ultra-resolution data through array tomography. Mapping larger brain tissue volumes (1 mm³) at high resolution is now within reach.

You can bring together data from large fields of view collected with a widefield microscope, such as ZEISS Axio Observer, with the ultrastructural information from a scanning electron microscope (SEM). ZEISS ZEN Connect software enables you to combine data from any ZEISS imaging source and observe interactions between different parts of the brain and the various neuronal cells involved.

The example shows an ultrathin mouse brain section. The overview image (left) was acquired with widefield microscopy. Synapsin-1 was labeled with Alexa Fluor 647 (green), which targets the pre-synaptic vesicles, and Alexa Fluor 594 labeled Gephyrin (red), which targets a part of the postsynaptic protein network. Nuclei were stained with DAPI (blue). The overview image was used for navigation and ROI relocation. The insets were acquired with scanning electron microscopy (right).

Optical clearing methods have enabled microscopy of fluorescently labeled neurons deep into brains. Light sheet microscopy, such as with ZEISS Lightsheet 7, or confocal microscopy, such as with the ZEISS LSM 9 family, enable you to achieve crisp, high resolution 3D imaging of neurons in cleared brains in a surprisingly short amount of time.