PUBLICATIONS/PREPRINTS

2018

Topological Skeletonization and Tree-Summarization of Neurons Using Discrete Morse Theory
Wang S, Li X, Mitra PP, Wang Y. (2018). arxiv:1805.04997.
Unidirectional monosynaptic connections from auditory areas to the primary visual cortex in the marmoset monkey
*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). bioRxiv 373779.
A High-throughput Neurohistological Pipeline for Brain-Wide Mesoscale Connectivity Mapping of the Common Marmoset
*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). bioRxiv 315804.
Continuity between koniocellular layers of dorsal lateral geniculate and inferior pulvinar nuclei in common marmosets
*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) biorxiv 315598.
Joint Atlas-Mapping of Multiple Histological Series combined with Multimodal MRI of Whole Marmoset Brains
Lee BC, Lin MK, Fu Y, Hata J, Miller MI, Mitra PP. (2018). arxiv:1805.04975.
On variational solutions for whole brain serial-section histology using the computational anatomy random orbit model
Lee BC, Tward DJ, Mitra PP, Miller MI. (2018) arxiv:1802.03453.
High precision automated detection of labeled nuclei in terabyte-scale whole-brain volumetric image data of mouse
Pahariya G, Das S, Jayakumar J, Bannerjee S, Vangala V, Ram K, Mitra PP. (2018) bioRxiv.252247.

2017

Brain-wide Maps Reveal Stereotyped Cell-Type-Based Cortical Architecture and Subcortical Sexual Dimorphism
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. Cell. 2017 Oct 5;171(2):456–469.e22.
The Active Atlas: Combining 3D Anatomical Models with Texture Detectors
Chen Y, McElvain L, Tolpygo A, Ferrante D, Karten H, Mitra PP, Kleinfeld D, Freund Y. (2017) arXiv:1702.08606.
Metrics for comparing neuronal tree shapes based on persistent homology
Li Y, Wang D, Ascoli GA, Mitra PP, Wang Y. PLoS ONE. 2017;12(8):e0182184.
Genetic Single Neuron Anatomy reveals fine granularity of cortical interneuron subtypes
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. bioRxiv 2017 Nov 20;:219485.
Performance of Image Matching in the Computational Anatomy Gateway: CPU and GPU Implementations in OpenCL
Tward DJ, Lee B, Mitra P, Miller MI. The Practice and Experience in Advanced Research Computing 2017. New York, New York, USA: ACM; 2017. 2 p.

2016

Comparative three-dimensional connectome map of motor cortical projections in the mouse brain
Jeong M, Kim Y, Kim J, Ferrante DD, Mitra PP, Osten P, Kim D. Scientific Reports. 2016 Feb 2;6(1):20072.
Towards a comprehensive atlas of cortical connections in a primate brain: Mapping tracer injection studies of the common marmoset into a reference digital template
Majka P, Chaplin TA, Yu H-H, Tolpygo A, Mitra PP, Wójcik DK, Rosa MGP. J Comp Neurol. 2016 Aug 1;524(11):2161–81.
Grand Challenges for Global Brain Sciences
Vogelstein JT, Amunts K, Andreou A, Angelaki D, Ascoli G, Bargmann C, et al. (2016) arXiv:1608.06548

2015

High-throughput method of whole-brain sectioning, using the tape-transfer technique
Pinskiy V, Jones J, Tolpygo A, Franciotti N, Weber K, Mitra PP. PLoS ONE 10(7): e0102363.
Brain-mapping projects using the common marmoset
Okano H, Mitra P. Neuroscience Research. 2015 Apr;93:3–7.

2014

The circuit architecture of whole brains at the mesoscopic scale
Mitra PP. Neuron. 2014 Sep 17;83(6):1273–83.
NSF workshop report: Discovering general principles of nervous system organization by comparing brain maps across species
Striedter GF, Belgard TG, Chen C-C, Davis FP, Finlay BL, Güntürkün O, et al. Journal of Comparative Neurology 2014 Mar 18;522(7):1445–53.

2013

A low-cost technique to cryo-protect and freeze rodent brains, precisely aligned to stereotaxic coordinates for whole-brain cryosectioning
Pinskiy V, Tolpygo AS, Jones J, Weber K, Franciotti N, Mitra PP.(2013) Journal Neuroscience Methods 218(2), 206-213.
Co-expression Profiling of Autism Genes in the Mouse Brain.
Menashe I, Grange P, Larsen EC, Banerjee-Basu S, Mitra PP (2013). PLOS Computational Biology, 9(7): e1003128.
Computational Neuroanatomy and Co-expression of Genes in the Adult Mouse Brain, Analysis Tools for the Allen Brain Atlas
Grange, P., Hawrylycz, M. & Mitra, P.P. Quantitative Biology (2013) 1: 91.

2012

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

2011

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

2010

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

2009

A Proposal for a Coordinated Effort for the Determination of Brainwide Neuroanatomical Connectivity in Model Organisms at a Mesoscopic Scale
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). PLoS Computational Biology. 5(3): e1000334.
The Brain Atlas Concordance Problem: Quantitative Comparison of Anatomical Parcellations
Bohland JW, Bokil H, Allen CB, Mitra PP. (2009) PLOS ONE 4(9): e7200.
An Anatomic Atlas of the Adult Mouse Brain
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). Nature Neuroscience 12(3), 356-362.

CONFERENCE PRESENTATIONS

2018

Toward the mesoscopic whole-brain neural connectivity in marmosets
Huo B-X, Lin MK, Takahashi YS, Hanada M, Nagashima J, Tolpygo AS, Lee BC, Miller MI, Rosa MGP, Okano H, Mitra PP. Oral symposium presented at: Winter Conference on Brain Research; 2018 Jan 14-19; Whistler, BC, Canada
Comprehensive image processing pipeline for marmoset brain connectivity mapping
Lin MK, Takahashi YS, Hanada M, Nagashima J, Huo B-X, Tolpygo AS, Lee BC, Miller MI, Rosa MGP, Okano H, Mitra PP. Poster session presented at: Japanese Society for Marmoset Research; 2018 Jan 16-18; Kyoto University, JP
Computational pipeline for marmoset brain connectivity mapping using injections of antero- and retrograde tracers on a brain-wide grid
Mitsutoshi H, Nagashima J, Takahashi YS, Lin MK, Huo B-X, Tolpygo AS, Rosa MGP, Okano H, Mitra PP. Poster session presented at: Japanese Society for Marmoset Research; 2018 Jan 16-18; Kyoto University, JP
A connectivity mapping of marmoset brain by an established computational image processing pipeline
Lin MK, Takahashi YS, Hanada M, Nagashima J, Huo B-X, Tolpygo AS, Lee BC, Miller MI, Rosa MGP, Okano H, Mitra PP. Poster session presented at: Japan Neuroscience Society; 2018 July 27-29; Kobe, JP

2017

Assembly of a High Efficiency Computational Pipeline for Marmoset Brain Mapping
Lin MK, Takahashi YS, Weber K, Huo B-X, Hanada M, Tolpygo AS, Ferrante D, Rosa MGP, Okano H, Mitra PP. Poster session presented at: Asia-Oceania Reginal Meeting for Marmoset Research; 2017 March 16-17; Seoul, ROK
Monosynaptic connections between auditory and visual areas in the marmoset monkey
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. Poster session presented at: Society for Neuroscience; 2017 Nov 11-15; Washington DC, USA

2016

Marmoset Brain Architecture Project: A high-throughput Neurohistological pipeline for Brain-wide Mesoscale connectivity mapping of Marmoset
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. Japan Neuroscience Society 2016
Computational infrastructure to enable whole-brain mesoscale circuit mapping for Marmoset
Lin MK, Takahashi YS, Weber K, Hossain K, Huo B, Tolpygo A, Ferrante DD, Bai S, Rosa MGP, Okano H, Mitra PP. Society for Neuroscience 2016. 470.01. San Diego, USA.
A high-throughput neurohistological pipeline for whole-brain mesoscale circuit mapping for Marmoset
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. Society for Neuroscience, 2016. San Diego, CA. Program No. 291.04.
Assembly of a High Efficiency Computational Pipeline for Marmoset Brain Mapping
Lin MK, Takahashi YS, Weber K, Huo B-X, Hanada M, Tolpygo AS, Ferrante D, Rosa MGP, Okano H, Mitra PP. Poster session presented at: Japanese Society for Marmoset Research; 2016 Dec 12-14; Tokyo, JP
Optimized Sequential Techniques for Marmoset Neural Circuit Mapping
Weber K, Lin MK, Takahashi YS, Hanada M, Huo B-X, Tolpygo AS, Ferrante D, Rosa MGP, Okano H, Mitra PP. Poster session presented at: Japanese Society for Marmoset Research; 2016 Dec 12-14; Tokyo, JP

2015

Workflow for mapping tracer injection studies of the common marmoset into a reference template
Majka, P., Chaplin, T.A., Yu, H.H., Tolpygo, A., Mitra, P.P., Wojcik, D.K., Rosa, M.G.P. Society for Neuroscience 2015, Chicago, I.L. 450.02
Dynamic control of forebrain by central thalamus
Lee, J., Liu, J., Lee, H., Weitz, A., Fang, Z., Lin, P., Fisher, R., Pinskiy, V., Tolpygo, A., Mitra, P., Schiff, N. Society for Neuroscience 2015, Chicago, I.L. 449.20

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
Carmel, J. B., Mechler, F., Mukherjee, A., Wen, T., Tolpygo, A., Mitra, P. (2014) Meeting of the Society for Neuroscience, Washington, D.C.
Combining brain clearing and light-sheet fluorescence microscopy with tape-transfer assisted sectioning and histochemistry for whole mouse brain and spinal cord imaging
Giese, G., Scherbarth, A., Pinskiy, V., Tolpygo, A., Mechler, F., Mitra, P. (2014) Meeting of the Society for Neuroscience, Washington, D.C.
The microanatomical origin of the high-field magnetic resonance imaging signal in the marmoset cerebral cortex: myelin sheaths or cell bodies?
Geyer, S., Reimann, K., Weiss, M., Rose, D., Silva, A. C., Rosa, M. G. P., Pinskiy, V., Tolpygo, A., Mitra, P. P., Turner, R. (2014). Meeting of the Society for Neuroscience, Washington, D.C.

2013

Dissecting long-range circuits in macaque cortex by registering optogenetically driven neural activity with anatomical connectivity
Shewcraft, R., Pinskiy, V., Tolpygo, A., Mukherjee, A., Putrino, D., Wong, Y. T., Mitra, P. P. (2013). Meeting of the Society for Neuroscience, San Diego, CA.
Software tools for reconstruction of 3D projection patterns for injection-based tractography
Mukherjee, A., Mechler, F., Pinsksiy, V., Tolpygo, A., Grange, P., Mitra, P. (2014) Meeting of the Society for Neuroscience, San Diego, CA.
Automated analysis of the density of monosynaptic inputs to VTA dopamine neurons
Grange, P., Mukherjee, A., Pinskiy, V., Tolpygo, A., Zheng, L., Uchida, N., Watabe-Uchida, M., Mitra, P. (2013). Meeting of the Society for Neuroscience, San Diego, CA.
Quantitative modeling of tracer injections into brain tissue
Sorooshyari, S., Pinskiy, V., Tolpygo, A., Mitra, P. (2013). Meeting of the Society for Neuroscience, San Diego, CA.
Combining high resolution mri and dti with dense whole-brain histology for mouse
Pinskiy, V., Mukherjee, A., Tolpygo, A., Badea, A., Johnson, A.G., Mitra, P. P. (2013). Meeting of the Society for Neuroscience, San Diego, CA.

Earlier

[ PDF ] : Carmel, J. B., Mechler, F., Mukherjee, A., Wen, T., Tolpygo, A., Mitra, P., 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 (2014). 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.

[ PDF ] : 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.

[ 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.

[ 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.

[ 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.

[ 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.

[ 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.

[ PDF ] : 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.Digital Atlas of the Zebra Finch Brain (Taeniopygia Guttata): a Dimensional and High Resolution Photo Atlas (2008). Meeting of the Society for Neuroscience, Washington, D.C.

[ PDF ] : 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.

[ PDF ] : 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.