Deep imaging, Brain-wide circuits, Neurophotonics
Deep imaging, Brain-wide circuits, Neurophotonics
(Title image: Ultrasound-encoded wavefront used for optical resolution imaging with diffuse light. See publications)
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 translucida, which has the smallest known vertebrate brain and shows fascinating behavior.
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.
Our lab is establishing the miniature fish Danionella translucida 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
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)
Kadobianskyi M, Papadopoulos IN, Chaigne T, Horstmeyer R, Judkewitz B. Scattering correlations of time-gated light, Optica 2018, 5(4):389-94
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
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
Judkewitz, B. Analysis of functional connectivity in the zebrafish olfactory bulb. Diploma Thesis (2005) supervised by Rainer Friedrich, Max Planck Institute for Medical Research, University of Heidelberg
Click here for the full publication list.
(Image: Simulated propagation of coherent light through brain tissue)
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 welcome applications as well as informal inquiries from highly motivated candidates at the undergraduate, PhD or postdoc level. Email Benjamin Judkewitz using this link.
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 Tegel Airport (TXL), the TXL bus will take you to our campus in 25 min (get off at Charité station). From Schönefeld Airport (SXF), take public transport to Berlin Hauptbahnhof (35 min ride and 5 min walk to our lab).
Our internal/campus address is Hufelandweg 14 (level 3, room 005). The building is marked by a blue 14 on this campus map. Alternatively, search Google Maps for "Hufelandweg 14, Berlin" or use the embedded map below.