Munich Cluster for Systems Neurology

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Nanoscale Hub

Electron Microscopic (EM) Hub

1.0 Objective
1.1 Organisation
1.2 Technical portfolio
1.3 Project request procedure
1.4 Fees
1.5 Publications


1.0 Objective

The Nanoscale hub has been established since 2017, not taking into account earlier logistic and administrative efforts or investments. It provides technical and scientific support for projects that require ultrastructural analysis. These include scientific questions that can't be addressed by light microscopy techniques due to resolution limitations. Typical examples within SyNergy comprise the characterization of neuronal, organellar, myelin, fibril or blood vessel morphologies or their context within tissue. Electron Microscopic (EM) investigations provide additional, non-hypothesis-driven insights. Currently, model organisms include mouse, zebrafish and human biopsies. The hub provides service and training for the whole workflow of Transmission (TEM) and Scanning EM (SEM) as well as Volume SEM. Image analysis support can only be provided to a limited extent. Depending on the project extent and complexity, either the Nanoscale Hub staff executes the work or trains scientists of the requesting SyNergy research group. SyNergy projects are prioritized but external project requests are considered depending on their general technical or scientific impact and benefit for future cluster-internal projects. The Nanoscale Hub integrates contiguous technologies, e.g. by collaborating with the Microscale Hub for correlative studies (CLEM). The Hub staff arranges contacts to groups with EM techniques that are not covered within the Hub.

Please contact the Nanoscale Hub staff for project requests or further questions (

1.1 Organisation


                          Location of the Nanoscale Hub in the DZNE

Name Function Location Mail phone
Martina Schifferer Hub group leader DZNE,
2G 157 089-4400-46487
Georg Kislinger Technical Assistant DZNE,
2G 148


Cornelia Niemann
Technical Assistant DZNE,
2G 148


SyNergy Coordinators

Name Institution
Martin Kerschensteiner Institute of Clinical Neuroimmunology –
Hospital and Biomedical Center of the Ludwig-Maximilians-University
Thomas Misgeld Institute of Neuronal Cell Biology (TUM-NCB)
German Center for Neurodegenerative Diseases (DZNE)
Mikael Simons Institute of Neuronal Cell Biology (TUM-NCB)
German Center for Neurodegenerative Diseases (DZNE)






1.2 Technical portfolio

• Sample processing (chemical fixation, HPF)
• TEM (Transmission Electron Microscopy)
• SEM (Scanning Electron Microscopy)
• ATUM (Automated Tape Collecting Ultramicrotomy)
• FIB-SEM (Focused Ion Beam SEM)
• Correlative EM (correlation strategy, EM part)
• Negative contrasting for in vitro studies



1.3 Project request procedure





Project request form
User policy form


1.4 Fees



1.5 Publications

Trifunctional lipid probes for comprehensive studies of single lipid species in living cells.
Höglinger D, Nadler A, Haberkant P, Kirkpatrick J, Schifferer M, Stein F, Hauke S, Porter FD, Schultz C. Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):1566-1571. doi: 10.1073/pnas.1611096114. Epub 2017 Feb 2

A Ratiometric Sensor for Imaging Insulin Secretion in Single β Cells.
Schifferer M, Yushchenko DA, Stein F, Bolbat A, Schultz C. Cell Chem Biol. 2017 Apr 20;24(4):525-531.e4. doi: 10.1016/j.chembiol.2017.03.001. Epub 2017 Mar 30. PMID: 28366620

Phase Separation of FUS Is Suppressed by Its Nuclear Import Receptor and Arginine Methylation.
Hofweber M, Hutten S, Bourgeois B, Spreitzer E, Niedner-Boblenz A, Schifferer M, Ruepp MD, Simons M, Niessing D, Madl T, Dormann D. Cell. 2018 Apr 19;173(3):706-719.e13. doi: 10.1016/j.cell.2018.03.004. PMID: 29677514

Iron-Sequestering Nanocompartments as Multiplexed Electron Microscopy Gene Reporters.
Sigmund F, Pettinger S, Kube M, Schneider F, Schifferer M, Schneider S, Efremova MV, Pujol-Martí J, Aichler M, Walch A, Misgeld T, Dietz H, Westmeyer GG. ACS Nano. 2019 Jul 23;13(7):8114-8123. doi: 10.1021/acsnano.9b03140. Epub 2019 Jun 13. PMID: 31194509

Two adhesive systems cooperatively regulate axon ensheathment and myelin growth in the CNS.
Djannatian M, Timmler S, Arends M, Luckner M, Weil MT, Alexopoulos I, Snaidero N, Schmid B, Misgeld T, Möbius W, Schifferer M, Peles E, Simons M. Nat Commun. 2019 Oct 22;10(1):4794. doi: 10.1038/s41467-019-12789-z. PMID: 31641127

Pro-inflammatory activation following demyelination is required for myelin clearance and oligodendrogenesis.
Cunha MI, Su M, Cantuti-Castelvetri L, Müller SA, Schifferer M, Djannatian M, Alexopoulos I, van der Meer F, Winkler A, van Ham TJ, Schmid B, Lichtenthaler SF, Stadelmann C, Simons M. J Exp Med. 2020 May 4;217(5):e20191390. doi: 10.1084/jem.20191390. PMID: 32078678

Multiscale ATUM-FIB Microscopy Enables Targeted Ultrastructural Analysis at Isotropic Resolution.
Kislinger G, Gnägi H, Kerschensteiner M, Simons M, Misgeld T, Schifferer M. iScience. 2020 Jul 24;23(7):101290. doi: 10.1016/j.isci.2020.101290. Epub 2020 Jun 20. PMID: 32622266

In vivo identification of apoptotic and extracellular vesicle-bound live cells using image-based deep learning.
Kranich J, Chlis NK, Rausch L, Latha A, Schifferer M, Kurz T, Foltyn-Arfa Kia A, Simons M, Theis FJ, Brocker T. J Extracell Vesicles. 2020 Jul 16;9(1):1792683. doi: 10.1080/20013078.2020.1792683. PMID: 32944180

Oligodendrocytes Provide Antioxidant Defense Function for Neurons by Secreting Ferritin Heavy Chain.
Mukherjee C, Kling T, Russo B, Miebach K, Kess E, Schifferer M, Pedro LD, Weikert U, Fard MK, Kannaiyan N, Rossner M, Aicher ML, Goebbels S, Nave KA, Krämer-Albers EM, Schneider A, Simons M. Cell Metab. 2020 Aug 4;32(2):259-272.e10. doi: 10.1016/j.cmet.2020.05.019. Epub 2020 Jun 11. PMID: 32531201

A Developmental Analysis of Juxtavascular Microglia Dynamics and Interactions with the Vasculature.
Mondo E, Becker SC, Kautzman AG, Schifferer M, Baer CE, Chen J, Huang EJ, Simons M, Schafer DP. J Neurosci. 2020 Aug 19;40(34):6503-6521. doi: 10.1523/JNEUROSCI.3006-19.2020. Epub 2020 Jul 13. PMID: 32661024

Myelin replacement triggered by single-cell demyelination in mouse cortex.
Snaidero N, Schifferer M, Mezydlo A, Zalc B, Kerschensteiner M, Misgeld T. Nat Commun. 2020 Sep 29;11(1):4901. doi: 10.1038/s41467-020-18632-0. PMID: 32994410

ATUM-FIB microscopy for targeting and multiscale imaging of rare events in mouse cortex.
Kislinger G, Gnägi H, Kerschensteiner M, Simons M, Misgeld T, Schifferer M. STAR Protoc. 2020 Dec 16;1(3):100232. doi: 10.1016/j.xpro.2020.100232. eCollection 2020 Dec 18. PMID: 33377119

Diet-dependent regulation of TGFβ impairs reparative innate immune responses after demyelination.
Bosch-Queralt M, Cantuti-Castelvetri L, Damkou A, Schifferer M, Schlepckow K, Alexopoulos I, Lütjohann D, Klose C, Vaculčiaková L, Masuda T, Prinz M, Monroe KM, Di Paolo G, Lewcock JW, Haass C, Simons M. Nat Metab. 2021 Feb;3(2):211-227. doi: 10.1038/s42255-021-00341-7. Epub 2021 Feb 18. PMID: 33619376

Loss of NPC1 enhances phagocytic uptake and impairs lipid trafficking in microglia.
Colombo A, Dinkel L, Müller SA, Sebastian Monasor L, Schifferer M, Cantuti-Castelvetri L, König J, Vidatic L, Bremova-Ertl T, Lieberman AP, Hecimovic S, Simons M, Lichtenthaler SF, Strupp M, Schneider SA, Tahirovic S. Nat Commun. 2021 Feb 24;12(1):1158. doi: 10.1038/s41467-021-21428-5. PMID: 33627648

Systematically defining selective autophagy receptor-specific cargo using autophagosome content profiling.
Zellner S, Schifferer M, Behrends C. Mol Cell. 2021 Mar 18;81(6):1337-1354.e8. doi: 10.1016/j.molcel.2021.01.009. Epub 2021 Feb 4. PMID: 33545068

White matter aging drives microglial diversity.
Safaiyan S, Besson-Girard S, Kaya T, Cantuti-Castelvetri L, Liu L, Ji H, Schifferer M, Gouna G, Usifo F, Kannaiyan N, Fitzner D, Xiang X, Rossner MJ, Brendel M, Gokce O, Simons M. Neuron. 2021 Apr 7;109(7):1100-1117.e10. doi: 10.1016/j.neuron.2021.01.027. Epub 2021 Feb 18. PMID: 33606969