SegEM: Efficient Image Analysis for High-Resolution Connectomics
- Manuel Berning, K. Boergens, M. Helmstaedter
- BiologyNeuron
- 23 September 2015
Dense connectomic reconstruction in layer 4 of the somatosensory cortex
- Alessandro Motta, Manuel Berning, M. Helmstaedter
- BiologyScience
- 3 November 2018
It is found that connectomic data alone allowed the definition of inhibitory axon types that showed established principles of synaptic specificity for subcellular postsynaptic compartments, but that at scales beyond ~5 μm, geometric predictability of the circuit structure was low and coarser models of random wiring needed to be rejected for dense cortical neuropil.
Axonal synapse sorting in medial entorhinal cortex
- H. Schmidt, Anjali Gour, Jakob Straehle, K. Boergens, M. Brecht, M. Helmstaedter
- BiologyNature
- 28 September 2017
Dense reconstructions from three-dimensional electron microscopy in rats reveal a cellular feedforward inhibition circuit involving wide, myelinated inhibitory axons and dendritic synapse clustering that can control the propagation of synchronized activity in the medial entorhinal cortex, which is known for temporally precise discharges.
webKnossos: efficient online 3D data annotation for connectomics
- K. Boergens, Manuel Berning, M. Helmstaedter
- Biology, Computer ScienceNature Methods
- 12 June 2017
We report webKnossos, an in-browser annotation tool for 3D electron microscopic data. webKnossos provides flight mode, a single-view egocentric reconstruction method enabling trained annotator crowds…
Cell-type specific innervation of cortical pyramidal cells at their apical dendrites
- Ali Karimi, J. Odenthal, F. Drawitsch, K. Boergens, M. Helmstaedter
- BiologyeLife
- 28 February 2020
Connectomic principles for the control of pyramidal cells at their apical dendrites are described and support differential computational properties of L2, L3 and subtypes of L5 pyramsidal cells in cortex.
Controlling FIB‐SBEM slice thickness by monitoring the transmitted ion beam
- K. Boergens, W. Denk
- PhysicsJournal of Microscopy
- 1 December 2013
It is found that the transmitted‐beam current decreases monotonically as the beam approaches the sample and can be used to determine the relative position of beam and sample to an accuracy of around one nanometre.
Postnatal connectomic development of inhibition in mouse barrel cortex
- Anjali Gour, K. Boergens, M. Helmstaedter
- BiologyScience
- 3 December 2020
The first comprehensive mapping of inhibitory circuit development in mammalian cortex provides quantitative insights into the formation of circuits and the precise time course for the establishment of synaptic target preference.
Full reconstruction of large lobula plate tangential cells in Drosophila from a 3D EM dataset
- K. Boergens, Christoph Kapfer, M. Helmstaedter, W. Denk, A. Borst
- BiologyPLoS ONE
- 28 November 2018
A dense reconstruction of lobula plate tangential cells of the fly Lobula plate is reconstructed, identifying the dorsal and the ventral centrifugal horizontal, dCH and vCH cell, as well as three VSlike cells, including their distinct dendritic and axonal projection area.
Cell-type specific innervation of cortical pyramidal cells at their apical tufts
- Ali Karimi, J. Odenthal, F. Drawitsch, K. Boergens, M. Helmstaedter
- BiologybioRxiv
- 15 March 2019
Connectomic principles for the control of pyramidal cells at their apical dendrites in the upper layers of the cerebral cortex are described and differential computational properties of layer 2, layer 3 and layer 5 pyramides cells in cortex are pointed to.
SynEM, automated synapse detection for connectomics
- B. Staffler, Manuel Berning, K. Boergens, Anjali Gour, Patrick van der Smagt, M. Helmstaedter
- BiologyeLife
- 14 July 2017
SynEM, a method for automated detection of synapses from conventionally en-bloc stained 3D electron microscopy image stacks, yields 97% precision and recall in binary cortical connectomes with no user interaction and removes the burden of manual synapse annotation for large densely mapped connectomes.
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