Konrad Rokicki

HortaCloud: An Open and Collaborative Platform for Whole Brain Neuronal Reconstructions

HortaCloud provides a cloud-based platform for collaborative whole-brain neuronal reconstruction from light microscopy data, enabling efficient analysis of large datasets without local hardware.

Deep-tissue spatial omics: imaging whole-embryo transcriptomics and subcellular structures at high spatial resolution

This paper introduces cycleHCR technology for high-resolution spatial transcriptomics and protein imaging in thick tissues, demonstrating its application in mouse embryos and brain slices.

A split-GAL4 driver line resource for Drosophila neuron types

The paper describes a collection of split-GAL4 driver lines for targeting specific neuron types in Drosophila, enabling functional and molecular studies.

Discovery of neuronal cell types by pairing whole cell reconstructions with RNA expression profiles

The paper introduces morphoFISH, a method combining imaging and spatial transcriptomics to identify new neuronal cell types in the mouse brain.

NeuronBridge: an intuitive web application for neuronal morphology search across large data sets

NeuronBridge enables rapid morphological matching of neurons across large datasets imaged with different modalities.

A searchable image resource of Drosophila GAL4-driver expression patterns with single neuron resolution

The paper provides a searchable image resource of Drosophila GAL4-driver expression patterns at single neuron resolution to improve cell type identification and split-GAL4 combination prediction.

Rapid reconstruction of neural circuits using tissue expansion and lattice light sheet microscopy

The paper develops a method to rapidly reconstruct neural circuits with single synapse resolution using tissue expansion and lattice light sheet microscopy, validated in Drosophila.

PatchPerPixMatch for Automated 3d Search of Neuronal Morphologies in Light Microscopy

PatchPerPixMatch automates 3D search for neuronal morphologies in Drosophila GAL4 line data by combining segmentation and efficient matching.

Expansion-Assisted Iterative-FISH defines lateral hypothalamus spatio-molecular organization

The paper introduces EASI-FISH, a method for spatial gene expression profiling in thick brain sections, and applies it to discover novel subregions in the lateral hypothalamus.

Reconstruction of 1,000 projection neurons reveals new cell types and organization of long-range connectivity in the mouse brain

The paper reconstructs 1,000 projection neurons in the mouse brain, revealing new cell types and organizational principles of long-range connectivity.