PUBLICATIONS/PREPRINTS

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 OpenCLThe 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

[Link] Mitra PP. (2014) The circuit architecture of whole brains at the mesoscopic scale. Neuron. 83(6):1273–83.

[Link] Striedter GF, Belgard TG, Chen C-C, Davis FP, Finlay BL, Güntürkün O, et al. (2014) NSF workshop report: Discovering general principles of nervous system organization by comparing brain maps across species. Journal of Comparative Neurology 2522(7):1445–53.

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 cryosectioningJournal 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 BrainPLOS Computational Biology9(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

[Link] Helmstaedter M, Mitra PP. (2012) Computational methods and challenges for large-scale circuit mapping. Opinion in Neurobiology. 22(1):162–9.

[PDF] Grange P, Mitra PP (2012). Computational Neuroanatomy and Gene Expression: Optimal Sets of Marker Genes for Brain Regions. IEEE, 46th annual Conference on Information Sciences and Systems, Princeton 2012.

2011

[Link] Grange P, Mitra PP. (2011) Algorithmic choice of coordinates for injections into the brain: encoding a neuroanatomical atlas on a grid. arXiv:1104.2616.

2010

[PDF] Bohland JW, Bokil H, Pathak SD, Lee CK, Ng L, Lau C, Kuan C, Hawrylycz M, Mitra PP (2010). Clustering of Spatial Gene Expression Patterns in the Mouse Brain, and Comparison with Classical Neuroanatomy. Methods 50 (2010) 105–112.

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

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. Poster session presented at: Society for Neuroscience, 2018. San Diego, CA.

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.

[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 templateSociety 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 thalamusSociety 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

PDF ] Pinskiy V, Krishnan K, Mukhopadhyay S, Collins Z, Tolpygo AS, Huang JZ, Mitra PP, High-Throughput Whole Brain Neuroanatomical mapping of GABAergic cell types in C57BL/6 mice (2011). Society for Neuroscience Meeting, Washington, DC.

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.