Connectomics
A Tiny Piece of the Connectome. Serial electron microscopy reconstruction of axonal inputs (various colors) onto a small segment of the apical dendrite (grey) of a pyramidal neuron in mouse cerebral cortex. The grey protrusions are dendritic spines. The arrows mark functional synapes, based on the presence of neurotransmitter-containing vesicles. {Courtesy of Bobby Kasthuri and Jeff Lichtman.}
The cerebral cortex of the human brain contains more than 160 trillion synapses, or sites of communication between neurons. Each neuron receives synaptic inputs from hundreds or even thousands of different neurons, and each sends outputs to a similar number of target neurons, spread out over a large distance. Thus, deciphering the “connectome,” or complete connectivity diagram, of even one type of neuron in the cortex poses enormous challenges.
Dr. Lichtman’s research focuses on the study of neural connectivity and how it changes as animals develop and age. With his colleagues he has developed a number of tools that permit synaptic level analysis of neural connections. These include activity dependent uptake of fluorescent dyes, transgenic approaches to label individual nerve cells, and “combinatoric” methods (e.g., DiOlistics, Brainbow, and NPS) to label many nerve cells in the same tissue. In addition, he has helped develop automated electron microscopy approaches for large scale neural circuit reconstruction. These connectomic methods seek to make it routine to acquire neural circuit data in any nervous system. The central focus of his work is to describe the ways in which developing nervous systems change to accommodate information that is acquired by experience.
The Lichtman Lab and Zhuang Lab in our center have been developing novel imaging methods to overcome these challenges. One method that the Lichtman Lab has optimized significantly in recent years is serial electron microscopy-based reconstruction of brain tissue. While it has for some time been possible to image ultrathin slices of brain tissue by electron microscopy and piece together three dimensional reconstructions, it’s an incredibly cumbersome process that has until recently allowed only very small, fragmented glimpses into connectome. But thanks to the recent acceleration of several steps in the pipeline from brain slicing and imaging to analysis, it’s now possible to reconstruct neural circuitry at a much more rapid pace and gain increasingly larger glimpses into the connectome.
Complementing this approach is a super-resolution light microscopy technique invented in the Zhuang lab - called stochastic optical reconstruction microscopy (STORM). This method allows fluorescent labeling and analysis of the molecular architecture of synapses at a resolution that is not possible with conventional light microscopy - in which, due to the diffraction of light, structures smaller than several hundred nanometers cannot be distinguished from one another. STORM overcomes this limitation by using photo-switchable fluorescent probes to temporally separate the otherwise spatially overlapping images of individual molecules, and it has recently been used by the Zhuang lab to begin mapping the precise synaptic fields of neurons.
As part of the Conte Center, the labs are using these, as well as viral tracing methods, to visualize the connectome of PV-cells in the prefrontal cortex, believed to be particularly vulnerable in mental illness. Of particular interest are changes in the PV-cell connectome across normal cortical development, and alternations in the PV-cell connectome in mouse models of early life stress or mental illness.
Podcast/video: The Microscopists, featuring Peter O’Toole interviewing Professor Jeff Lichtman (Dec 4, 2020)
https://www.youtube.com/watch?v=7MCSlkslVmk&t=4s
Podcast: “The Daily Experiment” for Gen Z (Aug 13 2020) with Mikey Taylor. click here to listen.
Recent Publications:
The Mind of a Mouse.
Abbott LF, Bock DD, Callaway EM, Denk W, Dulac C, Fairhall AL, Fiete I, Harris KM, Helmstaedter M, Jain* V, Kasthuri N, LeCun Y, Lichtman* JW, Littlewood PB, Luo L, Maunsell JHR, Reid RC, Rosen BR, Rubin GM, Sejnowski TJ, Seung HS, Svoboda K, Tank DW, Tsao D, Van Essen DC.
Cell. 2020 Sep 17;182:1372-1376. (* JWL and VJ, corresponding authors)
PMID: 32946777
Connectomes across development reveal principles of brain maturation in C. elegans
Witvliet D, Mulcahy B, Mitchell JK, Meirovitch Y, Berger DR, Wu Y, Liu Y, WX Koh, Parvathala R, Holmyard D, Schalek RL, Shavit N, Chisholm AD, Lichtman JW*, Samuel ADT*, Zhen M*.
bioRxiv 2020 doi: https://doi.org/10.1101/2020.04.30.066209
Long-Range Optogenetic Control of Axon Guidance Overcomes Developmental Boundaries and Defects.
Harris JM, Wang AY, Boulanger-Weill J, Santoriello C, Foianini S, Lichtman JW, Zon LI, Arlotta P.
Dev Cell. 2020 Jun 8;53:577-588.e7. doi: 10.1016/j.devcel.2020.05.009.
PMID: 32516597
An Individual Interneuron Participates in Many Kinds of Inhibition and Innervates Much of the Mouse Visual Thalamus.
Morgan JL, Lichtman JW.
Neuron. 2020 Feb 27. pii: S0896-6273(20)30100-8. doi: 10.1016/j.neuron.2020.02.001.
PMID:32142646
Multispectral tracing in densely labeled mouse brain with nTracer.
Roossien DH, Sadis BV, Yan Y, Webb JM, Min LY, Dizaji AS, Bogart LJ, Mazuski C, Huth RS, Stecher JS, Akula S, Shen F, Li Y, Xiao T, Vandenbrink M, Lichtman JW, Hensch TK, Herzog ED, Cai D.
Bioinformatics. 2019 Sep 15;35:3544-3546. doi: 10.1093/bioinformatics/btz084.
PMID:30715234
Developmental rewiring between cerebellar climbing fibers and Purkinje cells begins with positive feedback synapse addition.
Wilson AM, Schalek R, Suissa-Peleg A, Jones TR, Knowles-Barley S, Pfister H, Lichtman JW.
Cell Rep, 2019 Nov 26;29:2849-2861.e6. doi: 10.1016/j.celrep.2019.10.081.
PMID:31775050
Serial-section electron microscopy using automated tape-collecting ultramicrotome (ATUM).
Baena V, Schalek RL, Lichtman JW, Terasaki M.
Methods Cell Biol. 2019;152:41-67. doi: 10.1016/bs.mcb.2019.04.004. Epub 2019 Jun 8.
PMID: 31326026
Individual Oligodendrocytes Show Bias for Inhibitory Axons in the Neocortex.
Zonouzi M, Berger D, Jokhi V, Kedaigle A, Lichtman J, Arlotta P.
Cell Rep. 2019 Jun 4;27:2799-2808.e3. doi: 10.1016/j.celrep.2019.05.018.
PMID:31167127
Large-Area Fluorescence and Electron Microscopic Correlative Imaging With Multibeam Scanning Electron Microscopy.
Shibata S, Iseda T, Mitsuhashi T, Oka A, Shindo T, Moritoki N, Nagai T, Otsubo S, Inoue T, Sasaki E, Akazawa C, Takahashi T, Schalek R, Lichtman JW, Okano H.
Front Neural Circuits. 2019 May 8;13:29. doi: 10.3389/fncir.2019.00029. eCollection 2019.
PMID:31133819
Imaging Peripheral Nerve Regeneration: A New Technique for 3D Visualization of Axonal Behavior.
Leckenby JI, Chacon MA, Grobbelaar AO, Lichtman JW.
J Surg Res. 2019 Oct;242:207-213. doi: 10.1016/j.jss.2019.04.046. Epub 2019 May 11.
PMID:31085369
Multicolor multiscale brain imaging with chromatic multiphoton serial microscopy.
Abdeladim L, Matho KS, Clavreul S, Mahou P, Sintes JM, Solinas X, Arganda-Carreras I, Turney SG, Lichtman JW, Chessel A, Bemelmans AP, Loulier K, Supatto W, Livet J, Beaurepaire E.
Nature Commun. 2019 Apr 10;10(1):1662. doi: 10.1038/s41467-019-09552-9.
PMID:30971684
Development of the interscutularis model as an outcome measure for facial nerve surgery.
Leckenby JI, Chacon MA, Rolfe K, Lichtman JW, Grobbelaar AO.
Ann Anat. 2019 May;223:127-135. doi: 10.1016/j.aanat.2019.03.001. Epub 2019 Mar 22.
PMID:30910682
Nanobody immunostaining for correlated light and electron microscopy with preservation of ultrastructure.
Fang T, Lu X, Berger D, Gmeiner C, Cho J, Schalek R, Ploegh H, Lichtman J.
Nature Methods. 2018 Dec;15(12):1029-1032. doi: 10.1038/s41592-018-0177-x. Epub 2018 Nov 5.
Multispectral tracing in densely labeled mouse brain with nTracer.
Roossien DH, Sadis BV, Yan Y, Webb JM, Min LY, Dizaji AS, Bogart LJ, Mazuski C, Huth RS, Stecher JS, Akula S, Shen F, Li Y, Xiao T, Vandenbrink M, Lichtman JW, Hensch TK, Herzog ED, Cai D.
Bioinformatics. 2019 Sep 15;35(18):3544-3546. doi: 10.1093/bioinformatics/btz084.
PMID:30715234
VAST (Volume Annotation and Segmentation Tool): Efficient Manual and Semi-Automatic Labeling of Large 3D Image Stacks.
Berger DR, Seung HS, Lichtman JW.
Front Neural Circuits. 2018 Oct 16;12:88. doi: 10.3389/fncir.2018.00088. eCollection 2018.
PMID:30386216
Lamellar projections in the endolymphatic sac act as a relief valve to regulate inner ear pressure.
Swinburne IA, Mosaliganti KR, Upadhyayula S, Liu TL, Hildebrand DGC, Tsai TY, Chen A, Al-Obeidi E, Fass AK, Malhotra S, Engert F, Lichtman JW, Kirchhausen T, Betzig E, Megason SG.
eLife. 2018 Jun 19;7. pii: e37131. doi: 10.7554/eLife.37131.
PMID:29916365
Inhibitory circuit gating of auditory critical-period plasticity.
Takesian AE, Bogart LJ, Lichtman JW, Hensch TK.
Nature Neurosci. 2018 Feb;21(2):218-227. doi: 10.1038/s41593-017-0064-2. Epub 2018 Jan 22.
PMID:29358666
Digital tissue and what it may reveal about the brain.
Morgan JL, Lichtman JW.
BMC Biol. 2017 Oct 30;15(1):101. doi: 10.1186/s12915-017-0436-9
PMID:29084528
SnapShot: Tissue Clearing.
Richardson DS, Lichtman JW.
Cell. 2017 Oct 5;171(2):496-496.e1. doi: 10.1016/j.cell.2017.09.025.
PMID:28985569
Efficiency of Cathodoluminescence Emission by Nitrogen-Vacancy Color Centers in Nanodiamonds.
Zhang H, Glenn DR, Schalek R, Lichtman JW, Walsworth RL.
Small. 2017 Jun;13(22). doi: 10.1002/smll.201700543. Epub 2017 Apr 18.
PMID:28417543
Electron Microscopic Reconstruction of Functionally Identified Cells in a Neural Integrator.
Vishwanathan A, Daie K, Ramirez AD, Lichtman JW, Aksay ERF, Seung HS.
Curr Biol. 2017 Jul 24;27(14):2137-2147.e3. doi: 10.1016/j.cub.2017.06.028. Epub 2017 Jul 14
PMID:28712570
Identification of cellular diversity and neuronal network dynamics in long-term cultures of human brain organoids.
Quadrato G, Nguyen T, Macosko EZ, Sherwood JL, Yang SM, Berger D, Maria N, Scholvin J, Goldman M, Kinney J, Boyden ES, Lichtman J, Williams ZM, McCarroll SA, Arlotta P.
Nature, 2017 May 4;545(7652):48-53. doi: 10.1038/nature22047. Epub 2017 Apr 26
PMID:28445462
Whole-brain serial-section electron microscopy in larval zebrafish.
Hildebrand D, Torres R, Choi W, Quan T, Wetzel A, Plummer G, Portugues R, Bianco I, Randlett O, Saalfeld S, Baden A, Lillaney K, Burns R, Vogelstein J , Jeong W-K, Lichtman J, Cicconet M, Moon J, Champion A, Graham B, Schier A, Lee W-C, Engert F.
Nature, 2017 May 18;545(7654):345-349. doi: 10.1038/nature22356. Epub 2017 May 10.
PMID:28489821
Saturated Reconstruction of a Volume of Neocortex.
Kasthuri N, Hayworth KJ, Berger DR, Schalek RL, Conchello JA, Knowles-Barley S, Lee D, Vázquez-Reina A, Kaynig V, Jones TR, Roberts M, Morgan JL, Tapia JC, Seung HS, Roncal WG, Vogelstein JT, Burns R, Sussman DL, Priebe CE, Pfister H, Lichtman JW.
Cell. 2015 Jul 30;162(3):648-61. doi: 10.1016/j.cell.2015.06.054.
PMID: 26232230
Multispectral labeling technique to map many neighboring axonal projections in the same tissue.
Tsuriel S, Gudes S, Draft RW, Binshtok AM, Lichtman JW.
Nat Methods. 2015 Apr 27. doi: 10.1038/nmeth.3367. [Epub ahead of print]
PMID: 25915122
Correlative stochastic optical reconstruction microscopy and electron microscopy.
Kim D, Deerinck TJ, Sigal YM, Babcock HP, Ellisman MH, Zhuang X.
PLoS One. 2015 Apr 15;10(4):e0124581.
PMID:25874453
Ultrastructurally smooth thick partitioning and volume stitching for large-scale connectomics.
Hayworth KJ, Xu CS, Lu Z, Knott GW, Fetter RD, Tapia JC, Lichtman JW, Hess HF.
Nat Methods. 2015 Apr;12(4):319-22. doi: 10.1038/nmeth.3292. Epub 2015 Feb 16.
PMID: 25686390
The big data challenges of connectomics.
Lichtman JW, Pfister H, Shavit N.
Nat Neurosci. 2014 Nov;17(11):1448-54. doi: 10.1038/nn.3837. Epub 2014 Oct 28. Review.
PMID: 25349911
Imaging ATUM ultrathin section libraries with WaferMapper: a multi-scale approach to EM reconstruction of neural circuits.
Hayworth KJ, Morgan JL, Schalek R, Berger DR, Hildebrand DG, Lichtman JW.
Front Neural Circuits. 2014 Jun 27;8:68. doi: 10.3389/fncir.2014.00068. eCollection 2014.
PMID: 25018701
Exploring the connectome: petascale volume visualization of microscopy data streams.
Beyer J, Hadwiger M, Al-Awami A, Jeong WK, Kasthuri N, Lichtman JW, Pfister H.
IEEE Comput Graph Appl. 2013 Jul-Aug;33(4):50-61.
PMID: 24808059
Characterization and development of photoactivatable fluorescent proteins for single-molecule-based superresolution imaging.
Wang S, Moffitt JR, Dempsey GT, Xie XS, Zhuang X.
Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8452-7
PMID: 24912163
Distinct profiles of myelin distribution along single axons of pyramidal neurons in the neocortex.
Tomassy GS, Berger DR, Chen HH, Kasthuri N, Hayworth KJ, Vercelli A, Seung HS, Lichtman JW, Arlotta P.
Science. 2014 Apr 18;344(6181):319-24. doi: 10.1126/science.1249766.
PMID: 24744380
ConnectomeExplorer: query-guided visual analysis of large volumetric neuroscience data.
Beyer J, Al-Awami A, Kasthuri N, Lichtman JW, Pfister H, Hadwiger M.
IEEE Trans Vis Comput Graph. 2013 Dec;19(12):2868-77. doi: 10.1109/TVCG.2013.142.
PMID: 24051854
Improved tools for the Brainbow toolbox.
Cai D, Cohen KB, Luo T, Lichtman JW, Sanes JR.
Nat Methods. 2013 Jun;10(6):540-7.
PMID: 23866336
Why not connectomics?
Morgan JL, Lichtman JW.
Nat Methods. 2013 Jun;10(6):494-500.
PMID: 23722208
3D multicolor super-resolution imaging offers improved accuracy in neuron tracing.
Lakadamyali M, Babcock H, Bates M, Zhuang X, Lichtman J.
PLoS One. 2012;7(1):e30826.
PMID: 22292051