Judkewitz Lab
Brain-wide circuits, Acoustic communication, Microscopy
Judkewitz Lab
Brain-wide circuits, Acoustic communication, Microscopy
(Title image: Ultrasound-encoded wavefront used for optical resolution imaging with diffuse light. See publications)
News
About
Our everyday experience of the world is enabled by the interplay of large populations of neurons that are distributed across the brain. To understand their function, we need to study brain circuits with single cell resolution across large parts of the nervous system. This has been very challenging in vertebrates due to their size and opacity.
We are a group of neuroscientists, engineers, biologists and physicists who work on two complementary strategies to address this challenge and investigate brainwide circuits: First, we develop optical methods to tackle tissue opacity and push the depth limits of microscopy. Second, we are establishing a new vertebrate model organism, Danionella, which has the smallest known vertebrate brain and shows fascinating behavior.
Deep imaging
If our bodies were transparent, the implications for biomedical science would be tremendous. Biologists could directly look at deep tissues to study their function and doctors could diagnose diseases such as cancer by direct observation. Yet, many biological tissues are highly opaque due to diffuse scattering, which limits most optical techniques to superficial layers of tissue. As a result, despite many breakthroughs enabled by advances in optical imaging and optogenetics, these techniques are still severely handicapped by scattering.
We address this limitation by developing new optical approaches based on wavefront shaping, multiphoton microscopy and 'optical time reversal'. These techniques allow us access tissue depths that have long been outside the reach of microscopy.
Danionella
Our lab is establishing the miniature fish Danionella as a new model organism for neuroscience. We found it to have the smallest known adult vertebrate brain, containing an order of magnitude fewer neurons than zebrafish.
Despite their size, Danionella adults display many complex behaviors, including acoustic communication. Since our imaging methods can reach most of their brain volume, we believe that Danionella offer a unique opportunity to study the neuronal basis of vertebrate communication in a tractable circuit. After establishing transgenesis, seqeuencing the genome, and enabling CRISPR/Cas9 genome editing, we now investigate sensory as well as motor control of auditory communication with single-cell resolution at brain-wide scale. More here
Publications
Publications
Selected Publications
Veith J, Chaigne T, Svanidze A, Dressler LE, Hoffmann M, Gerhardt B, Judkewitz B: The mechanism for directional hearing in fish, Nature 2024, 631:118-124 (See also: News & Views article, Nature Podcast, Data, Code)
Böhm UL, Judkewitz B: Fast and light efficient remote focusing for volumetric voltage imaging, Nature Communications 2024, 15:9555
Berlage C, Böhm UL, Sanchez Moreno A, Ledderose J, Gidon A, Larkum ME, Plested A, Judkewitz B: High-speed three-dimensional random access scanning with a linear SLM, Optica 2024, 11(12):1639-1645,
Groneberg AH, Dressler LE, Hoffmann M, Kadobianskyi M, Müller J, Judkewitz B: Development of sound production in Danionella cerebrum, Journal of Experimental Biology 2024, 227(16):jeb247782 (or download the PDF here)
Cook VANO, Groneberg A, Hoffmann M, Kadobianskyi M, Veith J, Schulze L, Henninger J, Britz R, Judkewitz B: Ultrafast sound production mechanism in one of the smallest vertebrates, PNAS 2024, 121 (10) e2314017121
Hoffmann M, Henninger J, Veith J, Richter L, and Judkewitz B: Blazed oblique plane microscopy reveals scale-invariant inference of brain-wide population activity, Nature Communications 2023, 14:8019
Rajan G, Lafaye J, Carbo-Tano M, Duroure K, Faini G, Tanese D, Panier T, Candelier R, Henninger J, Britz R, Judkewitz B, Gebhardt C, Emiliani V, Debregeas G, Wyart C, Del Bene F: Evolutionary divergence of locomotion in two related vertebrate species, Cell Reports 2022, doi:10.1016/j.celrep.2022.110585
Berlage C, Tantirigama MLS, Babot M, Di Battista, Whitmire C, Papadopoulos IN, Poulet JFA, Larkum M, and Judkewitz B: Deep tissue scattering compensation with three-photon F-SHARP, Optica 2021, 8:1613-19
Papadopoulos IN, Jouhanneau JS, Takahashi N, Kaplan D, Larkum M, Poulet J and Judkewitz B: Dynamic conjugate F-SHARP microscopy, Light: Science & Applications 2020, 9:110
Kadobianskyi M, Schulze L, Schuelke M, Judkewitz B: Hybrid genome assembly and annotation of Danionella translucida, Scientific Data 2019, 6:156, (data at: NCBI SRA / GenBank / NCBI TSA – or more conveniently packaged: figshare)
Hoffmann M, Judkewitz B: Diffractive Oblique Plane Microscopy, Optica 2019, 6(9):1166-70
*Schulze L, *Henninger J, Kadobianskyi M, Chaigne T, Faustino AI, Hakiy N, Albadri S, Schuelke M, Maler L, Del Bene F, Judkewitz B: Transparent Danionella translucida as a genetically tractable vertebrate brain model, Nature Methods 2018, 15:977-83 (data on g-node) *: equal contribution
Kadobianskyi M, Papadopoulos IN, Chaigne T, Horstmeyer R, Judkewitz B. Scattering correlations of time-gated light, Optica 2018, 5(4):389-94
Hoffmann M, Papadopoulos IN, Judkewitz B. Kilohertz binary phase modulator for pulsed laser sources using a digital micromirror device, Optics Letters 2017, 43(1):22-25 (open access on arXiv)
Papadopoulos IN, Jouhanneau JS, Poulet JFA, Judkewitz B. Scattering compensation by focus scanning holographic aberration probing (F-SHARP), Nature Photonics 2017, 11:116-23
Judkewitz B, Horstmeyer R, Vellekoop IM, Papadopoulos IN, Yang C. Translation correlations in anisotropically scattering media, Nature Physics 2015, doi:10.1038/nphys3373; corresponding author: B.J. ; covered in a Nature Physics News & Views article
Zhou EH, Ruan H, Yang C, Judkewitz B, Focusing on moving targets through scattering samples, Optica 2014, 1(4):227-32
Judkewitz B *, Wang YM *, Horstmeyer R, Mathy A & Yang C. Speckle-scale focusing in the diffusive regime with time-reversal of variance-encoded light (TROVE), Nature Photonics 2013, 7(4):300-305; *first & corresponding author; covered in a Nature Photonics News & Views article
Wang YM *, Judkewitz B *, DiMarzio CA, & Yang C. Deep-tissue focal fluorescence imaging with digitally time-reversed ultrasound-encoded light. Nature Communications 2012, 3:928; *first & corresponding author
Wiechert MT, Judkewitz B, Riecke H, Friedrich RW, Mechanisms of pattern decorrelation by recurrent neuronal circuits, Nature Neuroscience 2010, 13 (8): 1003-1010
Judkewitz B, Rizzi M, Kitamura K, Häusser M, Targeted single-cell electroporation of mammalian neurons in vivo, Nature Protocols 2009, 4 (6): 862-869
*Kitamura K, *Judkewitz B, Kano M, Denk W, Häusser M, Targeted patch-clamp recordings and single-cell electroporation of unlabeled neurons in vivo, Nature Methods 2008, 5(1): 61-67; *shared first authorship
Porter J, Craven B, Khan RM, Chang SJ, Kang I, Judkewitz B, Volpe J, Settles G, Sobel N, Mechanisms of scent-tracking in humans, Nature Neuroscience 2007, 10 (1): 27-29
Yaksi E, Judkewitz B, Friedrich RW, Topological reorganization of odor representations in the olfactory bulb, PLoS Biology 2007, 5 (7): e178
Judkewitz B, Roth A, Häusser M, Dendritic enlightenment: using patterned two-photon uncaging to reveal the secrets of the brain's smallest dendrites (editorial/review), Neuron 2006, 50 (2): 180-183
Click here for the full publication list.
Team
Team
(Image: Simulated propagation of coherent light through brain tissue)
Alumni
Positions
Positions
Our group is highly interdisciplinary and brings together students and postdocs from a variety of subject areas, ranging from engineering and physical sciences to neuroscience and biology. We always welcome inquiries from highly motivated candidates at the undergraduate, PhD or postdoc level. Email Benjamin Judkewitz using this link.
Contact
Contact
Location
Our lab is based on the Charité and Humboldt University campus in Berlin Mitte. Located in the middle of town, we are within short walking distance from the central train station and easily reached by numerous public transport lines.
From BER Airport, take public transport (FEX, RE7 or S9 trains) to Berlin Hauptbahnhof (a 30-35 min ride and 5 min walk to our lab).
Our internal/campus address is Hufelandweg 14 (level 3, room 005). Search Google Maps for "Hufelandweg 14, Berlin" or use the embedded map below.
Postdoc