speckles.jpg
Judkewitz_cover.jpg
Screen Shot 2014-03-15 at 8.41.29 .png
speckles.jpg

Judkewitz Lab


Deep imaging, Brain-wide circuits, Neurophotonics

SCROLL DOWN

Judkewitz Lab


Deep imaging, Brain-wide circuits, Neurophotonics

(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

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

Böhm UL, Judkewitz B: Fast and light efficient remote focusing for volumetric voltage imaging, bioRxiv 2023, 2023.11.28.568783

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.

Judkewitz_cover.jpg

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.

Those interested in pursuing a PhD should also consider the PhD Fellowships by the Einstein Center for Neurosciences Berlin (which our lab is part of).

Screen Shot 2014-03-15 at 8.41.29 .png

Contact


Contact


Email

You can reach every lab member at ed.etirahc@[emantsal].[emantsrif] . Click here to send a message to Benjamin Judkewitz.

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.