Connectomics - Unraveling the Wiring of Neural Networks
Microscopy Applications for Live Sciences

Connectomics

Unraveling the Wiring of Neural Networks

Working in connectomics means creating comprehensive maps of brain and nervous system networks. Your research includes the identification and measurement of all parts of each neuron: the soma, dendrites, axonal path and branching patterns and combining that data with the synapses and gap junctions of the entire circuit.

Your microscopy challenges are extensive; submicron resolution is required over long distances inside large volumes of dense and complicated tissues.

Mouse brain synapses imaged using FIB-SEM tomography
Mouse brain synapses imaged using FIB-SEM tomography

Mouse brain synapses imaged using FIB-SEM tomography. Courtesy of A.Merchán Pérez, J.R. Rodriguez, L. Alonso-Nanclares, J. DeFelipe, Universidad Politécnica de Madrid, Spain

Mouse brain synapses imaged using FIB-SEM tomography. Courtesy of A.Merchán Pérez, J.R. Rodriguez, L. Alonso-Nanclares, J. DeFelipe, Universidad Politécnica de Madrid, Spain

Ultra-resolution 3D Imaging of Neurons

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.

Large mouse brain tissue section. Courtesy of J. Lichtman, Harvard University, USA
Large mouse brain tissue section. Courtesy of J. Lichtman, Harvard University, USA

Large mouse brain tissue section. Courtesy of J. Lichtman, Harvard University, USA

Large mouse brain tissue section. Courtesy of J. Lichtman, Harvard University, USA

Scanning Electron Microscopy at Record Speed

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.

Ultrathin mouse brain section. Courtesy of M. Ocana, Harvard University, USA
Ultrathin mouse brain section. Courtesy of M. Ocana, Harvard University, USA

Ultrathin mouse brain section. Courtesy of M. Ocana, Harvard University, USA

Ultrathin mouse brain section. Courtesy of M. Ocana, Harvard University, USA

Analyze Ultrastructural Information in a Wider Context

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).

Thy1-EGFP mouse brain cleared with a modified version of iDISCO
Thy1-EGFP mouse brain cleared with a modified version of iDISCO

Thy1-EGFP mouse brain cleared with a modified version of iDISCO, imaged with light sheet microscopy. Courtesy of S. Gandhi, University of California Irvine, USA, and Translucence Biosystems, USA

Thy1-EGFP mouse brain cleared with a modified version of iDISCO, imaged with light sheet microscopy. Courtesy of S. Gandhi, University of California Irvine, USA, and Translucence Biosystems, USA

Deep Imaging of Fluorescent Neurons with Optically Cleared Brain Tissue

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.

  • Mouse brain cleared with CLARITY.

    Neurons labeled with Thy1-GFP and acquired with confocal microscopy. Data set is 800 µm deep. Courtesy of T. Ruff, Max Planck Institute of Neurobiology, Germany

Contact ZEISS Microscopy

Contact

/4
Next Step:
  • Step 1
  • Step 2
  • Step 3
Contact us
Required Information
Optional Information

If you want to have more information on data processing at ZEISS please refer to our data privacy notice.

  • 1

    * The images shown on this page represent research content. ZEISS explicitly excludes the possibility of making a diagnosis or recommending treatment for possibly affected patients on the basis of the information generated with an Axioscan 7 slide scanner.