Daniel Raimund Berger

RAEM: random-access electron microscopy for revisitable 3D imaging

RAEM enables targeted, multi-resolution imaging of biological specimens by combining low-resolution 3D surveys with high-resolution imaging of specific regions.

Probing Molecular Diversity and Ultrastructure of Brain Cells with Fluorescent Aptamers

This paper introduces CAptVE, a method for fluorescent aptamer-based labeling that enables molecular analysis in ultrastructurally reconstructable electron micrographs.

Are Synaptic Clefts Directionally Oriented?

The paper analyzes synaptic cleft orientations in human and mouse brain data, finding directional biases that suggest mesoscale anisotropy in cortical layers.

SmartEM: machine-learning guided electron microscopy

SmartEM accelerates electron microscopy image acquisition by using machine learning to intelligently allocate imaging time, achieving up to 7-fold speedup in connectomic samples.

Developmental Connectomics of the Mouse Cerebellum

This study investigates synaptic connectivity development in the mouse cerebellum, revealing sequential input-dependent wiring and individualized parallel fiber inputs to Purkinje cells.

A connectomic resource for neural cataloguing and circuit dissection of the larval zebrafish brain

The paper presents a connectomic dataset of a larval zebrafish brain, enabling circuit analysis through synaptic and neuronal annotations.

EM-Compressor: Electron Microscopy Image Compression in Connectomics with Variational Autoencoders

EM-Compressor uses Variational Autoencoders to compress EM images for connectomics, reducing data size to 1/128th while preserving features needed for segmentation.

Extensive Soma-Soma Plate-Like Contact Sites (Ephapses) Connect Suprachiasmatic Nucleus Neurons

The paper identifies extensive soma-soma plate-like contacts (ephapses) between SCN neurons that may enable synchronization without chemical or electrical synapses.

A connectomic study of a petascale fragment of human cerebral cortex

The paper presents a connectomic analysis of a human cerebral cortex fragment, revealing structural and connectivity features of neurons and synapses.

Multi-Layered Maps of Neuropil with Segmentation-Guided Contrastive Learning

SegCLR, a self-supervised learning method, enables classification of cellular subcompartments and cell types from 3D electron microscopy data with minimal labeled data.

Mapping Alzheimer Disease Molecular Pathologies in Large-Scale Connectomics Data: A Publicly Accessible Correlative Microscopy Resource

The paper presents a vCLEM protocol to map Aβ and pTau in AD mouse hippocampus connectomics data, revealing new molecular and structural alterations.

A Scalable Staining Strategy for Whole-Brain Connectomics

The paper introduces a 12-step protocol called ODeCO to infiltrate osmium in whole mouse brains, preserving ultrastructure for connectome mapping.

Connectomics of the Octopus vulgaris vertical lobe provides insight into conserved and novel principles of a memory acquisition network

The paper analyzes the connectome of the Octopus vulgaris vertical lobe, identifying novel synaptic structures and functional roles in memory acquisition.

Multiplexed volumetric CLEM enabled by antibody derivatives provides new insights into the cytology of the mouse cerebellar cortex

The paper introduces a vCLEM method using fluorescent scFvs to combine molecular labeling with ssEM, revealing new cell types and subcellular features in mouse cerebellar cortex.

Post-embryonic maturation of the C. elegans motor circuit

The paper reconstructs the post-embryonic maturation of the C. elegans motor circuit using electron microscopy, showing how structural rewiring maintains functional output during development.

Neuromuscular connectomes across development reveal synaptic ordering rules

The paper traces neuromuscular connectivity in mice across development, revealing that synaptic pruning follows a global activity-based ordering rule.

Connectomes across development reveal principles of brain maturation

This study uses connectomics to show how brain circuits change with age in C. elegans, revealing principles of brain maturation through structural and functional remodeling.

Ultrastructural analysis of dendritic spine necks reveals a continuum of spine morphologies

The paper analyzes dendritic spine morphology using electron microscopy and computer vision, finding that spine shapes form a continuum rather than distinct categories.