PUBLICATIONS/PREPRINTS

[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] 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.

[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.

[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

[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.

[ 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

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

[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

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.

[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.