PUBLICATIONS/PREPRINTS

2020

[Link] Network (BICCN), Adkins RS, Aldridge AI, Allen S, Ament SA, An X, Mitra PP, et al.(2020) A multimodal cell census and atlas of the mammalian primary motor cortex. bioRxiv.

[Link] Network (BICCN), Muñoz-Castañeda R, Zingg B, Matho KS, Wang Q, Chen X, Foster NN, Mitra PP, et al. (2020) Cellular Anatomy of the Mouse Primary Motor Cortex | bioRxiv.

[Link] Wang D, Magee L, Huo B-X, Banerjee S, Li X, Jayakumar J, Lin MK, Ram K, Wang S, Wang Y, Mitra PP.(2020) Detection and skeletonization of single neurons and tracer injections using topological methods. arXiv:200402755 [Cs, Stat].

[Link] Matho KS, Huilgol D, Galbavy W, Kim G, He M, An X, Lu J, Wu P, Bella DJD, Shetty AS, Palaniswamy R, Hatfield J, Raudales R, Narasimhan A, Gamache E, Levine J, Tucciarone J, Mitra PP, Osten P, Arlotta P, Huang ZJ. (2020) Genetic dissection of glutamatergic neuron subpopulations and developmental trajectories in the cerebral cortex | bioRxiv.

[Link] Majka P, Bai S, Bakola S, Bednarek S, Chan JM, Jermakow N, Lauretta P, Reser DH, Theodoni P, Worthy KH, Wang XJ, Wojcik DK, Mitra PP, Rosa MGP. (2020)Open access resource for cellular-resolution analyses of corticocortical connectivity in the marmoset monkey. Nature Communications 2020;11:1133.

[Link] Banerjee S, Magee L, Wang D, Li X, Huo B-X, Jayakumar J, Matho K, Lin MK, Ram K, Sivaprakasam M, Huang J, Wang Y, Mitra PP.(2020) Semantic segmentation of microscopic neuroanatomical data by combining topological priors with encoder–decoder deep networks. Nature Machine Intelligence 2020;2:585–94.

[Link] Tward D, Li X, Huo B, Lee B, Miller MI, Mitra PP. (2020) Solving the where problem in neuroanatomy: a generative framework with learned mappings to register multimodal, incomplete data into a reference brain. bioRxiv 2020:2020.03.22.002618.

[Link] Lovell PV, Wirthlin M, Kaser T, Buckner AA, Carleton JB, Snider BR, McHugh AK, Tolpygo A, Mitra PP, Mello CV.(2020) ZEBrA: Zebra finch Expression Brain Atlas—A resource for comparative molecular neuroanatomy and brain evolution studies – Journal of Comparative Neurology – Wiley Online Library.

2019

[Link] *Lin MK, *Takahashi YS, Huo B-X, Hanada M, Nagashima J, Hata J, Tolpygo AS, Ram K, Lee BC, Miller MI, Rosa MGP, Sasaki E, Iriki A, Okano H, Mitra PP. (2019). A High-throughput Neurohistological Pipeline for Brain-Wide Mesoscale Connectivity Mapping of the Common Marmoset. elife 40042.

[Link] *Huo B-X, *Zeater N, Lin MK, Takahashi YS, Hanada M, Nagashima J, Lee BC, Grünert U, Miller MI, Rosa MGP, Okano H, Martin PR, Mitra PP. (2019) Relation of koniocellular layers of dorsal lateral geniculate to inferior pulvinar nuclei in common marmosets. European Journal of Neuroscience 14529.

[Link] Chen Y, McElvain LE, Tolpygo AS, Ferrante D, Friedman B, Mitra PP, Karten HJ, Freund Y, Kleinfeld D.(2019). An active texture-based digital atlas enables automated mapping of structures and markers across brains. Nature Methods 2019;16:341–50.

[Link] Kleinfeld D, Luan L, Mitra PP, Robinson JT, Sarpeshkar R, Shepard K, Xie C, Harris TD.(2019) Can One Concurrently Record Electrical Spikes from Every Neuron in a Mammalian Brain? Neuron 2019;103:1005–15.

[Link] Miller CT, Hale ME, Okano H, Okabe S, Mitra PP.(2019) Comparative Principles for Next-Generation Neuroscience. Front Behav Neurosci 2019;13:.

[Link] Griffin AD, Turtzo LC, Parikh GY, Tolpygo A, Lodato Z, Moses AD, Nair G, Perl DP, Edwards NA, Dardzinski BJ, Armstrong RC, Chaudhury AR, Mitra PP, Latour LL.(2019) Traumatic microbleeds suggest vascular injury and predict disability in traumatic brain injury. Brain 2019;142:3550–64.

[Link] Majka P, Rosa MGP, Bai S, Chan JM, Huo B-X, Jermakow N, Lin MK, Takahashi YS, Wolkowicz IH, Worthy KH, Rajan R, Reser DH, Wojcik DK, Okano H, Mitra PP. (2019) Unidirectional monosynaptic connections from auditory areas to the primary visual cortex in the marmoset monkey. Brain Struct Funct 2019;224:111–31.

2018

[Link] Lee BC, Tward DJ, Mitra PP, Miller MI. (2018) On variational solutions for whole brain serial-section histology using the computational anatomy random orbit model. PLOS Computational Biology.

[Link] *Rosa MGP, *Majka P, Bai S, Chan JM, Huo B-X, Jermakow N, Lin MK, Takahashi YS, Wolkowicz IH, Worthy KH, Rajan R, Reser DH, Wójcik DK, Okano H, Mitra PP. (2018). Unidirectional monosynaptic connections from auditory areas to the primary visual cortex in the marmoset monkey. Brain Structure and Function, 1-21.

[Link] Wang S, Li X, Mitra PP, Wang Y. (2018). Topological Skeletonization and Tree-Summarization of Neurons Using Discrete Morse Theory. arxiv:1805.04997.

[Link] *Lin MK, *Takahashi YS, Huo B-X, Hanada M, Nagashima J, Hata J, Tolpygo AS, Ram K, Lee BC, Miller MI, Rosa MGP, Sasaki E, Iriki A, Okano H, Mitra PP. (2018). A High-throughput Neurohistological Pipeline for Brain-Wide Mesoscale Connectivity Mapping of the Common Marmoset. bioRxiv 315804.

[Link] *Huo B-X, *Zeater N, Lin MK, Takahashi YS, Hanada M, Nagashima J, Lee BC, Grünert U, Miller MI, Rosa MGP, Okano H, Martin PR, Mitra PP. (2018) Continuity between koniocellular layers of dorsal lateral geniculate and inferior pulvinar nuclei in common marmosets. biorxiv 315598.

[Link] Lee BC, Lin MK, Fu Y, Hata J, Miller MI, Mitra PP. (2018). Joint Atlas-Mapping of Multiple Histological Series combined with Multimodal MRI of Whole Marmoset Brains. arxiv:1805.04975.

[Link] Pahariya G, Das S, Jayakumar J, Bannerjee S, Vangala V, Ram K, Mitra PP. (2018) High precision automated detection of labeled nuclei in terabyte-scale whole-brain volumetric image data of mouse. bioRxiv.252247.

2017

[Link] Kim Y, Yang GR, Pradhan K, Venkataraju KU, Bota M, García Del Molino LC, Fitzgerald G, Ram K, He M, Levine JM, Mitra PP, Huang ZJ, Wang X-J, Osten P. Brain-wide Maps Reveal Stereotyped Cell-Type-Based Cortical Architecture and Subcortical Sexual Dimorphism. Cell. 2017 Oct 5;171(2):456–469.e22.

[Link] Chen Y, McElvain L, Tolpygo A, Ferrante D, Karten H, Mitra PP, Kleinfeld D, Freund Y. (2017). The Active Atlas: Combining 3D Anatomical Models with Texture Detectors. arXiv:1702.08606.

[Link] Li Y, Wang D, Ascoli GA, Mitra PP, Wang Y. Metrics for comparing neuronal tree shapes based on persistent homology. PLoS ONE. 2017;12(8):e0182184.

[Link] Wang X, Tucciarone J, Jiang S, Yin F, Wang B-S, Wang D, Jia Y, Li Y, Yang T, Xu Z, Akram MA, Wang Y, Zeng S, Ascoli GA, Mitra P, Gong H, Luo Q, Huang ZJ. Genetic Single Neuron Anatomy reveals fine granularity of cortical interneuron subtypes. bioRxiv 2017 Nov 20;:219485.

[Link] Tward DJ, Lee B, Mitra P, Miller MI. Performance of Image Matching in the Computational Anatomy Gateway: CPU and GPU Implementations in OpenCL. The Practice and Experience in Advanced Research Computing 2017. New York, New York, USA: ACM; 2017. 2 p.

2016

[Link] *Jeong M, *Kim Y, Kim J, Ferrante DD, Mitra PP, Osten P, Kim D. Comparative three-dimensional connectome map of motor cortical projections in the mouse brain. Scientific Reports. 2016 Feb 2;6(1):20072.

[Link] Majka P, Chaplin TA, Yu H-H, Tolpygo A, Mitra PP, Wójcik DK, Rosa MGP. Towards a comprehensive atlas of cortical connections in a primate brain: Mapping tracer injection studies of the common marmoset into a reference digital template. Journal of Comparative Neurology 2016 Aug 1;524(11):2161–81.

[Link] Vogelstein JT, Amunts K, Andreou A, Angelaki D, Ascoli G, Bargmann C, et al. (2016) Grand Challenges for Global Brain Sciences. arXiv:1608.06548

2015

[Link] Pinskiy V, Jones J, Tolpygo A, Franciotti N, Weber K, Mitra PP (2015). High-throughput method of whole-brain sectioning, using the tape-transfer technique. PLoS ONE 10(7): e0102363.

[Link] Okano H, Mitra P. (2015) Brain-mapping projects using the common marmoset. Neuroscience Research. 93:3–7.

2014

2013

[Link] Pinskiy V, Tolpygo AS, Jones J, Weber K, Franciotti N, Mitra PP (2013). A low-cost technique to cryo-protect and freeze rodent brains, precisely aligned to stereotaxic coordinates for whole-brain cryosectioning. Journal Neuroscience Methods 218(2), 206-213.
[Link] Menashe I, Grange P, Larsen EC, Banerjee-Basu S, Mitra PP (2013). Co-expression Profiling of Autism Genes in the Mouse Brain. PLOS Computational Biology, 9(7): e1003128.

[Link] Grange, P., Hawrylycz, M. & Mitra, P.P. (2013) Computational Neuroanatomy and Co-expression of Genes in the Adult Mouse Brain, Analysis Tools for the Allen Brain Atlas. Quantitative Biology 1: 91.

2012

2011

2010

2009

[ PDF | Link] Bohland JW, Wu C, Barbas H, Bokil H, Cline HT, Freed PJ, Greenspan RJ, Haber SN, Hawrylycz M, Herrera DG, Hilgetag CC, Huang ZJ, Jones A, Jones EG, Karten HJ, Kleinfeld D, Kotter R, Lester HA, Lin JM, Mikula S, Panksepp J, Safdieh J, Saper CB, Schiff ND, Stillman BW, Svoboda K, Swanson LW, Toga AW, Watson JD, Mitra PP (2009). A Proposal for a Coordinated Effort for the Determination of Brainwide Neuroanatomical Connectivity in Model Organisms at a Mesoscopic Scale. PLoS Computational Biology. 5(3): e1000334.

[ PDF | Link ] : Bohland JW, Bokil H, Allen CB, Mitra PP. (2009) The brain atlas concordance problem: quantitative comparison of anatomical parcellations. PLoS One. 4(9).

[ PDF ] Ng L, Bernard A, Lau C, Overly CC, Dong HW, Kuan C, Pathak S, Sunkin SM, Dang C, Bohland JW, Bokil H, Mitra PP, Puelles L, Hohmann J, Anderson DJ, Lein ES, Jones AR & Hawrylycz M (2009). An Anatomic Atlas of the Adult Mouse Brain. Nature Neuroscience 12(3), 356-362.

CONFERENCE PRESENTATIONS

2018

Lee BC, Lin M, Hanada M, Nagashima J, Fu Y, Hata J, Huo B-X, Takahashi Y, Ram KK, Okano H, Mitra PP, Miller MI. (2018) An MRI-guided atlas-mapping of marmoset brain histology by and automatic registration method. Oral symposium presented at: Society for Neuroscience, 2018. San Diego, CA. Program No. 364.09.

Huo B-X, Zeater N, Lin MK, Takahashi YS, Hanada M, Nagashima J, Lee BC, Grünert U, Miller MI, Rosa MGP, Okano H, Martin PR, Mitra PP. (2018) Cortical connections of marmoset dorsal lateral geniculate nucleus and inferior pulvinar nuclei. Oral symposium presented at: Society for Neuroscience, 2018. San Diego, CA. Program No. 364.06.

Lin M, Hanada M, Lee BC, Takahashi YS, Huo B-X, Li X, Ram K, Shi B, Miller MI, Rosa MG, Okano H, Mitra PP. (2018) Towards a mesoscale connectivity map of the common marmoset: A partial connectivity matrix and an online data portal. Oral symposium presented at: Society for Neuroscience, 2018. San Diego, CA. Program No. 364.01.

Li X, Xu F, Ram K, Lin M, Huo B-X, Mitra PP. (2018) An integrated web based computational framework for terabyte size mesoscopic whole mouse brain data. Poster session presented at: Society for Neuroscience, 2018. San Diego, CA. Program No. 171.16.

Nagashima J, Hanada M, Lin M, Takahashi YS, Huo B-X, Tolpygo AS, Jayakumar J, Okano H, Mitra PP. (2018) A modified rapid silver stain technique in a high-throughput neurohistological pipeline. Poster session presented at: Society for Neuroscience, 2018. San Diego, CA. Program No. 171.14.

[Keynote] Huo B-X, Lin MK, Takahashi YS, Hanada M, Nagashima J, Tolpygo AS, Lee BC, Miller MI, Rosa MGP, Okano H, Mitra PP. Toward the mesoscopic whole-brain neural connectivity in marmosets. Oral symposium presented at: Winter Conference on Brain Research; 2018 Jan 14-19; Whistler, BC, Canada

Lin MK, Takahashi YS, Hanada M, Nagashima J, Huo B-X, Tolpygo AS, Lee BC, Miller MI, Rosa MGP, Okano H, Mitra PP. Comprehensive image processing pipeline for marmoset brain connectivity mapping. Poster session presented at: Japanese Society for Marmoset Research; 2018 Jan 16-18; Kyoto University, JP

Mitsutoshi H, Nagashima J, Takahashi YS, Lin MK, Huo B-X, Tolpygo AS, Rosa MGP, Okano H, Mitra PP. Computational pipeline for marmoset brain connectivity mapping using injections of antero- and retrograde tracers on a brain-wide grid. Poster session presented at: Japanese Society for Marmoset Research; 2018 Jan 16-18; Kyoto University, JP

[PDF] Lin MK, Takahashi YS, Hanada M, Nagashima J, Huo B-X, Tolpygo AS, Lee BC, Miller MI, Rosa MGP, Okano H, Mitra PP. A connectivity mapping of marmoset brain by an established computational image processing pipeline. Poster session presented at: Japan Neuroscience Society; 2018 July 27-29; Kobe, JP

2017

[PDF] Rosa MGP, Majka P, Worthy KH, Takahashi YS, Lin MK, Wolkowicz IH, Tolpygo AS, Bai S, Huo B-X, Chan JM, Sasaki E, Reser DH, Mitra PP. Monosynaptic connections between auditory and visual areas in the marmoset monkey. Poster session presented at: Society for Neuroscience; 2017 Nov 11-15; Washington DC, USA

[PDF] Lin MK, Takahashi YS, Weber K, Huo B-X, Hanada M, Tolpygo AS, Ferrante D, Rosa MGP, Okano H, Mitra PP. Assembly of a High Efficiency Computational Pipeline for Marmoset Brain Mapping. Poster session presented at: Asia-Oceania Reginal Meeting for Marmoset Research; 2017 March 16-17; Seoul, ROK

2016

Lin MK, Takahashi YS, Weber K, Huo B-X, Hanada M, Tolpygo AS, Ferrante D, Rosa MGP, Okano H, Mitra PP. Assembly of a High Efficiency Computational Pipeline for Marmoset Brain Mapping. Poster session presented at: Japanese Society for Marmoset Research; 2016 Dec 12-14; Tokyo, JP.

Weber K, Lin MK, Takahashi YS, Hanada M, Huo B-X, Tolpygo AS, Ferrante D, Rosa MGP, Okano H, Mitra PP. Optimized Sequential Techniques for Marmoset Neural Circuit Mapping. Poster session presented at: Japanese Society for Marmoset Research; 2016 Dec 12-14; Tokyo, JP

Mitra, P. P., Takahashi, Y. S., Weber, K., Lin, M. K., Hossain, K., Huo, B., Tolpygo, A. S., Ferrante, D. D., Hata, J., Chan, J., Mizukami, H., Watakabe, A., Yamamori, T., Kishi, N., Iriki, A., Rosa, M. G., Sasaki, E., Okano, H. A high-throughput neurohistological pipeline for whole-brain mesoscale circuit mapping for Marmoset. Oral presentation at: Society for Neuroscience, 2016. San Diego, CA. Program No. 291.04.

[PDF] Lin MK, Takahashi YS, Weber K, Hossain K, Huo B, Tolpygo A, Ferrante DD, Bai S, Rosa MGP, Okano H, Mitra PP. Computational infrastructure to enable whole-brain mesoscale circuit mapping for Marmoset. Poster session presented at: Society for Neuroscience 2016. 470.01. San Diego, USA.

[PDF] Lin MK, Takahashi YS, Hossain K, Huo B, Weber K, Tolpygo AS, Ferrante D, Hata J, Chan J, Watakabe A, Kishi N, Iriki A, Rosa MGP, Sasaki E, Okano H, Mitra PP. Marmoset Brain Architecture Project: A high-throughput Neurohistological pipeline for Brain-wide Mesoscale connectivity mapping of Marmoset. Poster session presented at: Japan Neuroscience Society 2016.

2015

[Link] Majka, P., Chaplin, T.A., Yu, H.H., Tolpygo, A., Mitra, P.P., Wojcik, D.K., Rosa, M.G.P. Workflow for mapping tracer injection studies of the common marmoset into a reference template. Society for Neuroscience 2015, Chicago, I.L. 450.02.

[Link] Lee, J., Liu, J., Lee, H., Weitz, A., Fang, Z., Lin, P., Fisher, R., Pinskiy, V., Tolpygo, A., Mitra, P., Schiff, N. Dynamic control of forebrain by central thalamus. Society for Neuroscience 2015, Chicago, I.L. 449.20.

2014

Carmel, J. B., Mechler, F., Mukherjee, A., Wen, T., Tolpygo, A., Mitra, P. (2014) Whole rat brain analysis of anterograde tracers from motor cortex and retrograde tracers from cervical spinal cord: Validation of an efficient, automated method with stereology. Meeting of the Society for Neuroscience, Washington, D.C.

[ PDF ] Giese, G., Scherbarth, A., Pinskiy, V., Tolpygo, A., Mechler, F., Mitra, P., Combining brain clearing and light-sheet fluorescence microscopy with tape-transfer assisted sectioning and histochemistry for whole mouse brain and spinal cord imaging (2014). Meeting of the Society for Neuroscience, Washington, D.C.

Geyer, S., Reimann, K., Weiss, M., Rose, D., Silva, A. C., Rosa, M. G. P., Pinskiy, V., Tolpygo, A., Mitra, P. P., Turner, R., The microanatomical origin of the high-field magnetic resonance imaging signal in the marmoset cerebral cortex: myelin sheaths or cell bodies? (2014). Meeting of the Society for Neuroscience, Washington, D.C.

2013

[ PDF ] : Shewcraft, R., Pinskiy, V., Tolpygo, A., Mukherjee, A., Putrino, D., Wong, Y. T., Mitra, P. P., Pesaran, B. Dissecting long-range circuits in macaque cortex by registering optogenetically driven neural activity with anatomical connectivity (2013). Meeting of the Society for Neuroscience, San Diego, CA.

[PDF ] : Mukherjee, A., Mechler, F., Pinsksiy, V., Tolpygo, A., Grange, P., Mitra, P. Software tools for reconstruction of 3D projection patterns for injection-based tractography (2013). Meeting of the Society for Neuroscience, San Diego, CA.

[ PDF ] : Grange, P., Mukherjee, A., Pinskiy, V., Tolpygo, A., Zheng, L., Uchida, N., Watabe-Uchida, M., Mitra, P. Automated analysis of the density of monosynaptic inputs to VTA dopamine neurons (2013). Meeting of the Society for Neuroscience, San Diego, CA.

[ PDF ] : Sorooshyari, S., Pinskiy, V., Tolpygo, A., Mitra, P. Quantitative modeling of tracer injections into brain tissue (2013). Meeting of the Society for Neuroscience, San Diego, CA.

[ PDF ] : Pinskiy, V., Mukherjee, A., Tolpygo, A., Badea, A., Johnson, A.G., Mitra, P. P. Combining high resolution mri and dti with dense whole-brain histology for mouse (2013). Meeting of the Society for Neuroscience, San Diego, CA.

2012

[ PDF ] Grange P., Bohland J. W., Hawrylycz, M., Mitra, P. P. A software suite for multivariate analysis of brain-wide gene-expression maps (2012). Meeting of the Society for Neuroscience, New Orleans, LA.

[ PDF ] Pinskiy V, Tolpygo AS, Franciotti N, Weber K, Mitra PP. Whole Skull and Spinal Cord Cryosectioning of Adult Mouse (2012). Meeting of the Society for Neuroscience, New Orleans, LA.

[ PDF ] Grange P, Okaty BW, Nelson SB, Hawrylycz M, Mitra PP, Distribution of cell types in the mouse brain from the Allen Atlas of the adult mouse brain (2012). Society for Neuroscience Meeting, Washington, DC.

[ PDF ] Mukhopadhyay S, Grange P, Sengupta A, Mitra PP, Inferences about brain evolution from brain-wide gene-expression maps (2012). Society for Neuroscience Meeting, Washington, DC.

2011

2010

[ PDF ] : Pinskiy V, Jones J, Wang H, Cox H, Mitra PP. Tape-transfer assisted cryosectioning for the Mouse Brain Architecture Project (2010). Meeting of the Society for Neuroscience, San Diego, CA.

[ PDF ] : Grange P, Pologruto T, Pinskiy V, Wang H, Khabbaz A, Spring S, Yu L, Germann J, Henkelman M, Mitra PP. Computer-guided stereotactic injections for the Mouse Brain Architecture Project (2010). Meeting of the Society for Neuroscience, San Diego, CA.

[ PDF ] : Grange P and Mitra PP. Marker genes and the anatomy of the mouse brain (2010). Meeting of the Society for Neuroscience, San Diego, CA.

2008

[ PDF ] Bohland JW, Bokil, H Pathak S, Lin JM, Lee CK, Ng L, Osorio-Duque F, Lau C, Herrera D, Hawrylycz M, Mitra PP. Clustering of spatial gene expression patterns in the mouse brain and comparison with classical neuroanatomy (2008). Meeting of the Society for Neuroscience, Washington, D.C.

[ PDF ] Bokil H, Bohland JW, Pathak S, Lin JM, Lee CK, Ng L, Osorio-Duque F, Lau C, Herrera D, Hawrylycz M, Mitra PP. Spatial correlation and localization patterns of gene expression in the mouse brain (2008). Meeting of the Society for Neuroscience, Washington, D.C.

Lin JM, Bohland JW, Andrews PA, Iossifov I, Yankama B, Kulkarni J, Wu C, Berwick RC, Di Sciullo AM, Mitra PP. A literature mining and curation system for neuroscience knowledge discovery (2008). Meeting of the Society for Neuroscience, Washington, D.C.

[PPT] Karten HJ, Brzozowska-Prechtl A, Prechtl J, Wang H, Mitra PP (2008) Digital Atlas of the Zebra Finch Brain (Taeniopygia Guttata): a Dimensional and High Resolution Photo Atlas, Society for Neuroscience 2008.

2007

Bohland JW, Bokil H, Wu C, Breiter HC, Makris N, Kennedy DN, Allen CB, Mitra PP. Quantitative comparison of anatomical parcellation schemes for MRI (2007). Meeting of the Society for Neuroscience, San Diego, CA.

Lin JM, Andrews PA, Burns GA, Bohland JW, Allen CB, Mitra PP. Community structure of neuroscience research: inferences from a co-authorship graph of Society for Neuroscience meeting abstracts (2007). Meeting of the Society for Neuroscience, San Diego, CA.