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Employment (3)

Janelia Research Campus: Ashburn, US

2018-06-01 to present | Group Leader (Computation and Theory)
Employment
Source: Self-asserted source
Jan Funke

UPC: Barcelona, ES

2015-08-01 to 2018-05-31 | Post-Doctoral Researcher (Institut de Robòtica i Informàtica Industrial)
Employment
Source: Self-asserted source
Jan Funke

ETH Zürich: Zurich, CH

2014-08-01 to 2015-07-31 | Post-Doctoral Researcher (Institute of Neuroinformatics)
Employment
Source: Self-asserted source
Jan Funke

Education and qualifications (2)

ETH Zürich: Zurich, CH

2010-10-01 to 2014-07-31 | Doctor of Science (Institute of Neuroinformatics)
Education
Source: Self-asserted source
Jan Funke

TU Dresden: Dresden, DE

2005-10-01 to 2010-09-01 | Diploma (master-equivalent) (Informatik)
Education
Source: Self-asserted source
Jan Funke

Funding (4)

Behavioural strategies and neural mechanisms for robust navigation

2023-01-01 to present | Grant
Deutsche Forschungsgemeinschaft (Bonn, DE)
URL: https://app.dimensions.ai/details/grant/grant.13558246
GRANT_NUMBER: 513850388
Source: Self-asserted source
Jan Funke via DimensionsWizard

Candidate-Based Segmentation Methods for Biomedical Image Processing

2016-09-01 to 2018-02-28 | Grant
Swiss National Science Foundation (Bern, CH)
URL: https://app.dimensions.ai/details/grant/grant.5492930
GRANT_NUMBER: 165241
Source: Self-asserted source
Jan Funke via DimensionsWizard

Neuron Reconstruction from Electron Microscopy Images

2013-12-01 to 2017-05-31 | Grant
Swiss National Science Foundation (Bern, CH)
URL: https://app.dimensions.ai/details/grant/grant.5235387
GRANT_NUMBER: 149861
Source: Self-asserted source
Jan Funke via DimensionsWizard

Neural Circuit Reconstruction

2011-01-01 to 2014-12-31 | Grant
Swiss National Science Foundation (Bern, CH)
URL: https://app.dimensions.ai/details/grant/grant.5223679
GRANT_NUMBER: 130470
Source: Self-asserted source
Jan Funke via DimensionsWizard

Works (50 of 61)

Items per page:
Page 1 of 2

Discriminative Attribution Dataset A

Janelia Research Campus
2025 | Dataset
DOI: 10.25378/janelia.28143944.v1
Contributors: Diane Adjavon; Nils Eckstein; Jan Funke
Source: check_circle
DataCite

Discriminative Attribution Dataset A

Janelia Research Campus
2025 | Dataset
DOI: 10.25378/janelia.28143944
Contributors: Diane Adjavon; Nils Eckstein; Jan Funke
Source: check_circle
DataCite

Discriminative Attribution Dataset B

Janelia Research Campus
2025 | Dataset
DOI: 10.25378/janelia.28163624
Contributors: Diane Adjavon; Nils Eckstein; Jan Funke
Source: check_circle
DataCite

Discriminative Attribution Dataset B

Janelia Research Campus
2025 | Dataset
DOI: 10.25378/janelia.28163624.v1
Contributors: Diane Adjavon; Nils Eckstein; Jan Funke
Source: check_circle
DataCite

CellMap 2024 Segmentation Challenge

Janelia Research Campus
2024 | Other
DOI: 10.25378/janelia.c.7456966
Contributors: CellMap Project Team; David Ackerman; Misha B. Ahrens; Yoshinori Aso; Emma Avetissian; Davis Bennett; Christopher Karl Ernst Bleck; John Bogovic; Marley Bryant; Daniel Crooks et al.
Source: check_circle
DataCite

CellMap Segmentation Challenge

Janelia Research Campus
2024 | Other
DOI: 10.25378/janelia.28034561.v1
Contributors: CellMap Project Team; David G. Ackerman; Misha B. Ahrens; Yoshinori Aso; Emma Avetissian; Davis Bennett; Christopher Karl Ernst Bleck; John Bogovic; Marley Bryant; Daniel Crooks et al.
Source: check_circle
DataCite

CellMap Segmentation Challenge

Janelia Research Campus
2024 | Other
DOI: 10.25378/janelia.28034561
Contributors: CellMap Project Team; David G. Ackerman; Misha B. Ahrens; Yoshinori Aso; Emma Avetissian; Davis Bennett; Christopher Karl Ernst Bleck; John Bogovic; Marley Bryant; Daniel Crooks et al.
Source: check_circle
DataCite

Neural-circuit basis of song preference learning in fruit flies.

iScience
2024-06 | Journal article
DOI: 10.1016/j.isci.2024.110266
PMID: 39040064
PMC: PMC11260866
Contributors: Imoto K; Ishikawa Y; Aso Y; Funke J; Tanaka R; Kamikouchi A
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Neurotransmitter classification from electron microscopy images at synaptic sites in Drosophila melanogaster.

Cell
2024-05 | Journal article
DOI: 10.1016/j.cell.2024.03.016
PMID: 38729112
PMC: PMC11106717
Contributors: Eckstein N; Bates AS; Champion A; Du M; Yin Y; Schlegel P; Lu AK; Rymer T; Finley-May S; Paterson T et al.
Source: Self-asserted source
Jan Funke via Europe PubMed Central

A Bayesian Solution to Count the Number of Molecules within a Diffraction Limited Spot

2024-04 | Preprint
DOI: 10.1101/2024.04.18.590066
PPR: PPR841208
Contributors: Hillsley A; Stein J; Tillberg PW; Stern DL; Funke J
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Connectome-driven neural inventory of a complete visual system

2024-04 | Preprint
DOI: 10.1101/2024.04.16.589741
PPR: PPR838937
Contributors: Nern A; Loesche F; Takemura S; Burnett LE; Dreher M; Gruntman E; Hoeller J; Huang GB; Januszewski M; Klapoetke NC et al.
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Model-based inference of synaptic plasticity rules

2023-12 | Preprint
DOI: 10.1101/2023.12.11.571103
PPR: PPR772395
Contributors: Mehta Y; Tyulmankov D; Rajagopalan AE; Turner GC; Fitzgerald JE; Funke J
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Neural-circuit basis of song preference learning in fruit flies

2023-10 | Preprint
DOI: 10.1101/2023.10.24.563693
PPR: PPR748669
Contributors: Imoto K; Ishikawa Y; Aso Y; Funke J; Tanaka R; Kamikouchi A
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Network Statistics of the Whole-Brain Connectome of<i>Drosophila</i>

2023-07 | Preprint
DOI: 10.1101/2023.07.29.551086
PPR: PPR699005
Contributors: Lin A; Yang R; Dorkenwald S; Matsliah A; Sterling AR; Schlegel P; Yu S; McKellar CE; Costa M; Eichler K et al.
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Towards Generalizable Organelle Segmentation in Volume Electron Microscopy.

Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada
2023-07 | Journal article
DOI: 10.1093/micmic/ozad067.487
PMID: 37613645
Contributors: Heinrich L; Patton W; Bennett D; Ackerman D; Park G; Bogovic JA; Eckstein N; Petruncio A; Clements J; Pang S et al.
Source: Self-asserted source
Jan Funke via Europe PubMed Central

A Connectome of the Male<i>Drosophila</i>Ventral Nerve Cord

2023-06 | Preprint
DOI: 10.1101/2023.06.05.543757
PPR: PPR671346
Contributors: Takemura S; Hayworth KJ; Huang GB; Januszewski M; Lu Z; Marin EC; Preibisch S; Xu CS; Bogovic J; Champion AS et al.
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Neuronal wiring diagram of an adult brain

2023-06 | Preprint
DOI: 10.1101/2023.06.27.546656
PPR: PPR684467
Contributors: Dorkenwald S; Matsliah A; Sterling AR; Schlegel P; Yu S; McKellar CE; Lin A; Costa M; Eichler K; Yin Y et al.
Source: Self-asserted source
Jan Funke via Europe PubMed Central

A leaky integrate-and-fire computational model based on the connectome of the entire adult<i>Drosophila</i>brain reveals insights into sensorimotor processing

2023-05 | Preprint
DOI: 10.1101/2023.05.02.539144
PPR: PPR653992
Contributors: Shiu PK; Sterne GR; Spiller N; Franconville R; Sandoval A; Zhou J; Simha N; Kang CH; Yu S; Kim JS et al.
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Publisher Correction: Structured cerebellar connectivity supports resilient pattern separation.

Nature
2023-02 | Journal article
DOI: 10.1038/s41586-023-05703-7
PMID: 36631615
Contributors: Nguyen TM; Thomas LA; Rhoades JL; Ricchi I; Yuan XC; Sheridan A; Hildebrand DGC; Funke J; Regehr WG; Lee WA
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Hierarchical architecture of dopaminergic circuits enables second-order conditioning in <i>Drosophila</i>.

eLife
2023-01 | Journal article
DOI: 10.7554/elife.79042
PMID: 36692262
PMC: PMC9937650
Contributors: Yamada D; Bushey D; Li F; Hibbard KL; Sammons M; Funke J; Litwin-Kumar A; Hige T; Aso Y
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Local shape descriptors for neuron segmentation.

Nature methods
2022-12 | Journal article
DOI: 10.1038/s41592-022-01711-z
PMID: 36585455
PMC: PMC9911350
Contributors: Sheridan A; Nguyen TM; Deb D; Lee WA; Saalfeld S; Turaga SC; Manor U; Funke J
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Structured cerebellar connectivity supports resilient pattern separation.

Nature
2022-11 | Journal article
DOI: 10.1038/s41586-022-05471-w
PMID: 36418404
PMC: PMC10324966
Contributors: Nguyen TM; Thomas LA; Rhoades JL; Ricchi I; Yuan XC; Sheridan A; Hildebrand DGC; Funke J; Regehr WG; Lee WA
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations.

Nature biotechnology
2022-09 | Journal article
DOI: 10.1038/s41587-022-01427-7
PMID: 36065022
PMC: PMC7614077
Contributors: Malin-Mayor C; Hirsch P; Guignard L; McDole K; Wan Y; Lemon WC; Kainmueller D; Keller PJ; Preibisch S; Funke J
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Transverse endoplasmic reticulum expansion in hereditary spastic paraplegia corticospinal axons.

Human molecular genetics
2022-08 | Journal article
DOI: 10.1093/hmg/ddac072
PMID: 35348668
Contributors: Zhu PP; Hung HF; Batchenkova N; Nixon-Abell J; Henderson J; Zheng P; Renvoisé B; Pang S; Xu CS; Saalfeld S et al.
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Neural network organization for courtship-song feature detection in Drosophila.

Current biology : CB
2022-07 | Journal article
DOI: 10.1016/j.cub.2022.06.019
PMID: 35793679
PMC: PMC9378594
Contributors: Baker CA; McKellar C; Pang R; Nern A; Dorkenwald S; Pacheco DA; Eckstein N; Funke J; Dickson BJ; Murthy M
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Hierarchical architecture of dopaminergic circuits enables second-order conditioning in <i>Drosophila</i>

2022-03 | Preprint
DOI: 10.1101/2022.03.30.486484
PPR: PPR476281
Contributors: Yamada D; Yamada D; Bushey D; Feng L; Hibbard K; Sammons M; Funke J; Litwin-Kumar A; Hige T; Aso Y
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Structured connectivity in the cerebellum enables noise-resilient pattern separation

2021-11 | Preprint
DOI: 10.1101/2021.11.29.470455
PPR: PPR426256
Contributors: Nguyen TM; Thomas LA; Rhoades JL; Ricchi I; Yuan XC; Sheridan A; Hildebrand DGC; Funke J; Regehr WG; Lee WA
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Whole-cell organelle segmentation in volume electron microscopy.

Nature
2021-10 | Journal article
DOI: 10.1038/s41586-021-03977-3
PMID: 34616042
Contributors: Heinrich L; Bennett D; Ackerman D; Park W; Bogovic J; Eckstein N; Petruncio A; Clements J; Pang S; Xu CS et al.
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Automated Reconstruction of Whole-Embryo Cell Lineages by Learning from Sparse Annotations

2021-07 | Preprint
DOI: 10.1101/2021.07.28.454016
PPR: PPR376533
Contributors: Malin-Mayor C; Hirsch P; Guignard L; McDole K; Wan Y; Lemon WC; Keller PJ; Preibisch S; Funke J
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Ultrastructural readout of in vivo synaptic activity for functional connectomics

2021-07 | Preprint
DOI: 10.1101/2021.07.07.451278
PPR: PPR366263
Contributors: Simon A; Roth A; Sheridan A; Fişek M; Marra V; Racca C; Funke J; Staras K; Häusser M
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Automatic detection of synaptic partners in a whole-brain Drosophila electron microscopy data set.

Nature methods
2021-06 | Journal article
DOI: 10.1038/s41592-021-01183-7
PMID: 34168373
PMC: PMC7611460
Contributors: Buhmann J; Sheridan A; Malin-Mayor C; Schlegel P; Gerhard S; Kazimiers T; Krause R; Nguyen TM; Heinrich L; Lee WA et al.
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Which image-based phenotypes are most promising for using AI to understand cellular functions and why?

Cell systems
2021-05 | Journal article
DOI: 10.1016/j.cels.2021.04.012
PMID: 34015259
Contributors: Lundberg E; Funke J; Uhlmann V; Gerlich D; Walter T; Carpenter A; Coehlo LP
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Local Shape Descriptors for Neuron Segmentation

2021-01 | Preprint
DOI: 10.1101/2021.01.18.427039
PPR: PPR267918
Contributors: Sheridan A; Nguyen T; Deb D; Lee WA; Saalfeld S; Turaga S; Manor U; Funke J
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Reconstruction of motor control circuits in adult Drosophila using automated transmission electron microscopy.

Cell
2021-01 | Journal article
DOI: 10.1016/j.cell.2020.12.013
PMID: 33400916
PMC: PMC8312698
Contributors: Phelps JS; Hildebrand DGC; Graham BJ; Kuan AT; Thomas LA; Nguyen TM; Buhmann J; Azevedo AW; Sustar A; Agrawal S et al.
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Automatic whole cell organelle segmentation in volumetric electron microscopy

2020-11 | Preprint
DOI: 10.1101/2020.11.14.382143
PPR: PPR238854
Contributors: Heinrich L; Bennett D; Ackerman D; Park W; Bogovic J; Eckstein N; Petruncio A; Clements J; Xu CS; Funke J et al.
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Neural Network Organization for Courtship Song Feature Detection inDrosophila

2020-10 | Preprint
DOI: 10.1101/2020.10.08.332148
PPR: PPR224322
Contributors: Baker CA; McKellar C; Nern A; Dorkenwald S; Pacheco DA; Pang R; Eckstein N; Funke J; Dickson BJ; Murthy M
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Dense neuronal reconstruction through X-ray holographic nano-tomography.

Nature neuroscience
2020-09 | Journal article
DOI: 10.1038/s41593-020-0704-9
PMID: 32929244
PMC: PMC8354006
Contributors: Kuan AT; Phelps JS; Thomas LA; Nguyen TM; Han J; Chen CL; Azevedo AW; Tuthill JC; Funke J; Cloetens P et al.
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Neurotransmitter Classification from Electron Microscopy Images at Synaptic Sites in Drosophila

2020-06 | Preprint
DOI: 10.1101/2020.06.12.148775
PPR: PPR175468
Contributors: Eckstein N; Bates AS; Du M; Hartenstein V; Jefferis GS; Funke J
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Reconstruction of motor control circuits in adult Drosophila using automated transmission electron microscopy

2020-01 | Preprint
DOI: 10.1101/2020.01.10.902478
PPR: PPR108432
Contributors: Maniates-Selvin JT; Hildebrand DGC; Graham BJ; Kuan AT; Thomas LA; Nguyen T; Buhmann J; Azevedo AW; Shanny BL; Funke J et al.
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Automatic Detection of Synaptic Partners in a Whole-Brain Drosophila EM Dataset

2019-12 | Preprint
DOI: 10.1101/2019.12.12.874172
PPR: PPR105645
Contributors: Buhmann J; Sheridan A; Gerhard S; Krause R; Nguyen T; Heinrich L; Schlegel P; Lee WA; Wilson R; Saalfeld S et al.
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Synaptic Cleft Segmentation in Non-Isotropic Volume Electron Microscopy of the Complete Drosophila Brain

arXiv preprint arXiv:1805.02718
2018 | Journal article
Source: Self-asserted source
Jan Funke

The candidate multi-cut for cell segmentation

Biomedical Imaging (ISBI 2018), 2018 IEEE 15th International Symposium on
2018 | Conference paper
Source: Self-asserted source
Jan Funke

Analyzing Image Segmentation for Connectomics.

Frontiers in neural circuits
2018-11 | Journal article
DOI: 10.3389/fncir.2018.00102
PMID: 30483069
PMC: PMC6243088
Contributors: Plaza SM; Funke J
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Large Scale Image Segmentation with Structured Loss Based Deep Learning for Connectome Reconstruction.

IEEE transactions on pattern analysis and machine intelligence
2018-05 | Journal article
DOI: 10.1109/tpami.2018.2835450
PMID: 29993708
Contributors: Funke J; Tschopp F; Grisaitis W; Sheridan A; Singh C; Saalfeld S; Turaga SC
Source: Self-asserted source
Jan Funke via Europe PubMed Central

A Deep Structured Learning Approach Towards Automating Connectome Reconstruction from 3D Electron Micrographs

arXiv preprint arXiv:1709.02974
2017 | Journal article
Source: Self-asserted source
Jan Funke

TED: A Tolerant Edit Distance for segmentation evaluation

Methods
2017 | Journal article
Source: Self-asserted source
Jan Funke

TED: A Tolerant Edit Distance for segmentation evaluation.

Methods (San Diego, Calif.)
2017-01 | Journal article
DOI: 10.1016/j.ymeth.2016.12.013
PMID: 28108198
Contributors: Funke J; Klein J; Moreno-Noguer F; Cardona A; Cook M
Source: Self-asserted source
Jan Funke via Europe PubMed Central

Accurate and linear time pose estimation from points and lines

European Conference on Computer Vision
2016 | Conference paper
Source: Self-asserted source
Jan Funke

Efficient convolutional neural networks for pixelwise classification on heterogeneous hardware systems

ISBI
2016 | Conference paper
Source: Self-asserted source
Jan Funke

Structured learning of assignment models for neuron reconstruction to minimize topological errors

Biomedical Imaging (ISBI), 2016 IEEE 13th International Symposium on
2016 | Conference paper
Source: Self-asserted source
Jan Funke
Items per page:
Page 1 of 2

Peer review (6 reviews for 6 publications/grants)

Review activity for F1000Research. (1)
Review activity for International journal of computer vision. (1)
Review activity for Nature biotechnology. (1)
Review activity for Nature computational science. (1)
Review activity for Nature machine intelligence. (1)
Review activity for Nature methods. (1)
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