Journal Publications
PRE-PRINTS UNDER REVIEW
Z. S. Navabi, R. Peters, B. Gulner, A. Cherkkil, E. Ko, F. Dadashi, J. O'Brien, M. Feldkamp, S. B. Kodandaramaiah, Computer vision guided rapid and precise automated cranial microsurgeries in rodents (under review), Pre-print: Biorxiv 2024
J. Hu, A. Cherkkil, D. A. Surinach, I. Oladepo, R. Hossain, S. Fausner, K. Saxena, E. Ko, R. Peters, M. Feldkamp, P. C Konda, V. Pathak, R. Horstmeyer, S. B. Kodandaramaiah, Pan-cortical cellular imaging in freely behaving mice using a miniaturized micro-camera array microscope (mini-MCAM), (Under review), Biorxiv 2024
D Surinach, ML Rynes, K Saxena, E Ko, AD Redish, SB Kodandaramaiah, Strategy dependent recruitment of distributed cortical circuits during spatial navigation (under review) Biorxiv 2023
M L Streng, R E Carter, B W Kottke, K Togneri, E Wasserman, V Rajendran, EKrook-Magnuson, S B Kodandaramaiah, T J Ebner, Mesoscale Ca2+ imaging reveals networks of Purkinje cell dendritic and somatic modulation, with divergent roles of activity versus correlation during behavior (under review), Biorxiv 2023
B. R. Gulner, Z. S. Navabi, S. B. Kodandaramaiah, 3D morphometric analysis of mouse skulls using microcomputed tomography and computer vision (under review), Pre-print: Biorxiv 2022
PUBLISHED
J. Hope, T. Beckerle, P. Cheng, Z. Viavattine, M. Feldkamp, S. Fausner, K.Saxena, E. Ko, I. Hryb, R.E. Carter, T. J. Ebner, S. B. Kodandaramaiah, Brain-wide neural recordings in mice navigating physical spaces enabled by a cranial exoskeleton, Nature Methods 2024
Kodandaramaiah, D. Aharoni, E. A. Gibson, Special Section Guest Editorial: Open-source neurophotonic tools for neuroscience, S. B., Neurophotonics, 2024
I. Oladepo, K. Saxena, D. Surinach, M. Lehman, S. B. Kodandaramaiah, Computer vision guided open-source active commutator for neural imaging in freely behaving animals, Neurophotonics 2024
A D Alegria, A S Joshi, J B Mendana, K Khosla, K Smith, B Tiberius Auch, M Donovan, J Bischof, D Gohl, S B Kodandaramaiah, A machine vision guided robot for fully automated embryonic microinjection, Genetics 2024
Z. Guo, N. Zuchowicz, J. Bouwmeester, A. S. Joshi, A. L. Neisch, K. Smith, J. Daly, M. L. Etheridge, E. B. Finger, S. B. Kodandaramaiah, T. S. Hays, M. Hagedorn, J. C. Bischof, Conduction‐Dominated Cryomesh for Organism Vitrification, Advanced Science 2024
S. W. Cramer*, S. P. Haley*, L. S. Popa*, E. Scott, R. E. Carter, J. Dominguez, J. D. Aronson2, L. Sable, E. B. Flaherty, L. Sabal, D. Surinach, C. C. Chen, S. B. Kodandaramaiah, T. J. Ebner, Effects of mild, repetitive traumatic brain injury on cortical functional connectivity in the mouse, J Neurobiology of Diseases 2023, *Equal Contribution
J. Hu*, R. F. Hossain*, Z. S. Navabi, A. Tillery, M. Laroque, P. D. Donaldson, S. L. Swisher, S. B. Kodandaramaiah, Stencil-printed, Flexible Graphene Electrocorticography (ECoG) Arrays J Neural Engineering 2023, *Equal Contribution
A. K. Nietz, L. S. Popa, M. L. Streng, R. E. Carter, S. B. Kodandaramaiah and T. J. Ebner, Wide-field Calcium Imaging of Neuronal Network Dynamics, Biology 2022
P.D. Donaldson*, Z. S. Navabi*, R. E. Carter, S. Fausner, L. Ghanbari, T. J. Ebner, S. L. Swisher^, S. B. Kodandaramaiah^, Polymer skulls with integrated transparent electrode arrays for cortex-wide opto-electrophysiological recordings, Advanced Healthcare Materials, 2022 *Equal Contribution, ^co-corresponding authors
S. L. West, J. Aronson, L. S. Popa, R. E. Carter, A. Shekhar, K. D. Feller, L. Ghanbari, S. B. Kodandaramaiah, T. J. Ebner, Wide-Field Calcium Imaging of Dynamic Cortical Networks During Locomotion, Cerebral Cortex, 2021
M. L. Rynes*, D. Surinach*, S. Linn, M. Laroque, V. Rajendran, J. Dominguez, O. Hadjistamoulou, Z. S. Navabi, L. Ghanbari, G. W. Johnson, M. Nazari, M. Mohajerani, S. B. Kodandaramaiah, Miniaturized head-mounted device for whole cortex mesoscale imaging in freely behaving mice, Nature Methods 2021 *Equal Contribution
S. W. Cramer, R. E. Carter, J. D.Aronson, S B.Kodandaramaiah, T. J. Ebner, C. C. Chen, Through the looking glass: a review of cranial window technology for optical access to the brain, Journal of Neuroscience Methods, 2021, https://doi.org/10.1016/j.jneumeth.2021.109100
G. Shull, C. Haffner, W. B Huttner, E. Taverna, S. B. Kodandaramaiah, Manipulation of single neural stem cells and neurons in brain slices using robotic microinjection, Journal of Visualized experiments 2021 (Video Link)
A. Alegria, A. Joshi, J. O’Brien, S. B. Kodandaramaiah, Single neuron recording: progress towards high-throughput analysis, Bioelectronics in Medicine, 17 Sep 2020
M. L. Rynes, L. Ghanbari, D. Sousa Schulman, S. Linn, M. Laroque, J. Dominguez, Z. S. Navabi, P. Sherman & S. B. Kodandaramaiah, Assembly and operation of an open-source, computer numerical controlled (CNC) robot for performing cranial microsurgical procedures, Nature Protocols, 2020
G. Shull, C. Haffner, W. B Huttner, E. Taverna, S. B. Kodandaramaiah, Robotic platform for microinjection into single cells in intact tissue, EMBO Reports, 2019
G. Holst, W. A. Stoy, B. Yang, I. Kolb, S. B. Kodandaramaiah, L. Li, U. Knoblich, H. Zeng, B. Haider, E. S. Boyden, C. R. Forest, Autonomous patch clamp robot for functional characterization of neurons in vivo: development and application to mouse visual cortex, Journal of Neurophysiology, 2019
L. Ghanbari, R. E. Carter, M. L. Rynes, J. Dominguez, G. Chen, A. Naik, J. Hu, M. A. K. Sagar, L. Haltom, N. Mossazghi, M. M. Gray, S. L. West, K. W. Eliceiri, T. J. Ebner, S. B. Kodandaramaiah, Cortex-wide neural interfacing via transparent polymer skulls, Nature Communications, 2019
L. Ghanbari*, M. L. Rynes*, J. Hu, D. Sousa Schulman, G. W. Johnson, M. Laroque, G. M. Shull, S. B. Kodandaramaiah, Craniobot: A computer numerical controlled robot for cranial microsurgeries, Scientific Reports, 2019 *Equal Contribution
B. D. Allen, C. Moore-Kochlacs, J. G. Bernstein, J. Kinney, J. Scholvin, L. Seoane, C. Chronopoulos, C. Lamantia, S. B. Kodandaramaiah, M. Tegmark and E. S. Boyden, Automated in vivo patch clamp evaluation of extracellular multielectrode array spike recording capability, J Neurophysiology, 2018
S. B. Kodandaramaiah*, F. J. Flores*, G. L. Holst, A. C. Singer, X. Han , E. N. Brown, E. S. Boyden^, C. R. Forest^ Multi-neuron intracellular recording in vivo via interacting autopatching robots, Elife 2018, *Equal Contribution, ^Co-corresponding Authors
H. J. Suk, I. Van Welie, S. B. Kodandaramaiah, B. D. Allen, C. R. Forest, E. S. Boyden, Closed-loop real-time imaging enables fully automated cell-targeted patch-clamp neural recording in vivo, Neuron, 2017
K. D. Piatkevich, H. J. Suk, S. B. Kodandaramaiah, F. Yoshida, E. M. DeGennaro, M. Drobizhev, T. E. Hughes, R. Desimone, E. S Boyden, V. V. Verkhusha, Near-infrared fluorescent proteins engineered from bacterial phytochromes in neuroimaging, Biophysical Journal, 2017
I. Kolb, G. Talei Franzesi, M. Wang, S. B. Kodandaramaiah, C. R. Forest, E. S. Boyden, and A. C. Singer, Evidence for long-timescale patterns of synaptic inputs in CA1 of awake behaving mice, J Neuroscience, 2017
N. Grossman, D. Bono, N. Dedic, S. B. Kodandaramaiah, A. Rudenko, H. Suk, A. M. Cassara, E. Neufeld, N. Kuster, L. Tsai, A. Pascual-Leone, E. S. Boyden, Noninvasive deep brain stimulation via temporally interfering electric fields, Cell, 2017
A. C. Singer, G. Talei Franzesi, S. B. Kodandaramaiah, F. J. Flores, J. D. Cohen, A. K. Lee, C. Börgers, C. R. Forest, N. J. Kopell, E. S. Boyden, Mesoscale-duration activated states gate spiking in response to fast rises in membrane voltage in the awake brain, J Neurophysiology, 2017
Q. Wu, I. Kolb, B. Callahan, Z. Su, W. Stoy, S. B. Kodandaramaiah, R. Neve, H. Zeng, E.S. Boyden, C. R. Forest, and Alexander Chubykin, Integration of autopatching with automated pipette and cell detection in vitro, J Neurophysiology, 2016
S. B. Kodandaramaiah, I. R. Wickersham, G. B. Holst, A. C. Singer, G. Talei-Franzesi, C. R. Forest, E. S. Boyden, Assembly and operation of the autopatcher for automated intracellular neural recording in vivo, Nature Protocols, 2016
M. V. Baratta, S. B. Kodandaramaiah, P. E. Monahan, P. A. Lin, K. Kim, A. Yang C. R. Forest, E. S. Boyden, K. A. Goosens, Stress enables reinforcement-elicited serotonergic consolidation of fear memory, Biological Psychiatry, 2015
R. R. Harrison, I. Kolb, S. B. Kodandaramaiah, A. A. Chubykin, A. Yang, M. F. Bear, E. S. Boyden, C. R. Forest, Microchip amplifier for in vitro, in vivo, and automated whole-cell patch-clamp recording, J Neurophysiology, 2014
A. S. Chuong, M. L. Miri*, V. Busskamp*, G. A. C. Matthews*, L. C. Acker*, A. T. Sorensen, A. Young, N. C. Klapoetke, M. A. Henninger, S. B. Kodandaramaiah, M. Ogawa, S. B. Ramanlal, R. C. Bandler, B. D. Allen, C. R. Forest, B. Y. Chow, X. Han, Y. Lin, K. M. Tye, R. Roska, J. A. Cardin, E. S. Boyden, Noninvasive optical inhibition with a red-shifted microbial rhodopsin, Nature Neuroscience, 2014 *Equal Contribution
S. B. Kodandaramaiah, E. S. Boyden and C. R. Forest, In vivo robotics: towards the automation of neuroscience and other intact-system biological fields, Annals of NYAS, 2013
S. B. Kodandaramaiah, G. Talei Franzesi, B. Y. Chow, E. S. Boyden, C. R. Forest, Automated whole-cell patch clamp electrophysiology of neurons in vivo, Nature Methods, 2012
PEER-reviewed Conference Proceedings
1) L. Ghanbari, R. Carter, M. Rynes, J. Dominguez, G. Chen, J.Hu, T. Ebner, S. B. Kodandaramaiah, See-Shells: Transparent Polymer Skulls for Pan-Cortical Neural Interfacing, 9th International IEEE EMBS Conference on Neural Engineering, San Francisco, CA, March 20th-23rd, 2019
2) P. Donaldson, L. Ghanbari, M. Rynes, S. B. Kodandaramaiah, S. Swisher, Inkjet-Printed Silver Electrode Array for In-Vivo Electrocorticography, 9th International IEEE EMBS Conference on Neural Engineering, San Francisco, CA, March 20th-23rd, 2019
3) J. An, F. J. Flores, S. B. Kodandaramaiah, I. D. Betta, K. Nikolaeva, E. S. Boyden, C. R. Forest, E. N. Brown, Automated Assessment of Loss of Consciousness Using Whisker and Paw Movements During Anesthetic Dosing in Head-Fixed Rodents, 2018 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) Honolulu, HI
4) G. Shull, J. Hu, J. Buschnyj, H. Koon, J. Abel, S. B. Kodandaramaiah, Shape Memory Alloy Actuatable Woven Neural Probes, ASME 2018 Conference on Smart Materials, Adaptive Structures and Intelligent Systems, San Antonio, TX
5) L. Ghanbari, R. Carter, M. Rynes, J. Dominguez, J. Hu, N. Mossazghi, M. Laroque, T. Ebner, S. B. Kodandaramaiah, Brain Windows: Digitally Generated 3D Cranial Windows for Pan Cortical Neural Interfacing, Proceedings of the 2017 Design of Medical Devices Conference, Minneapolis, MN, April 10th-12th, 2018
6) G.Shull, C. Haffner, W. Huttner, S. B. Kodandaramaiah, E. Taverna, A robot for high throughput analysis of neural stem cells in intact tissue, Proceedings of the 2017 Design of Medical Devices Conference, Minneapolis, MN, April 10th-12th, 2018
7) M. Rynes, L. Ghanbari, J. Hu, D. S. Schulman, G. Johnson, M. Laroque, S. B. Kodandaramaiah, Principles of Computer Numerical Control Applied to Small Animal Microsurgical Procedures, Proceedings of the 2017 Design of Medical Devices Conference, Minneapolis, MN, April 10th-12th, 2018
8) G. Johnson, L.Lehto, S. Mangia, O. Gröhn, S. Michaeli, S. B. Kodandaramaiah, Conceptual Design of Flex-DBS, a Mechanically Reconfigurable Deep Brain Stimulation Probe, Proceedings of the 2017 Design of Medical Devices Conference, Minneapolis, MN, April 11th-13th, 2017
9) B. D. Allen, C. Moore-Kochlacs, J. Scholvin, J. B. Kinney, J. Bernstein, S. B. Kodandaramaiah, N. Kopell, E. S. Boyden, Towards ground truth in ultra-dense neural recording, Proceedings of the Computational and Systems Neuroscience (Cosyne) Meeting 2016, Salt Lake City, UT, February 25 - 28, 2016.
10) A. Singer, G.T. Franzesi, S. B. Kodandaramaiah, F. Flores, C. Forest, N. Kopell, E. Boyden, Interaction of Slow Network Integration and Fast Neural Integration Towards Spike Generation, Proceedings of the Computational and Systems Neuroscience (Cosyne) Meeting 2015, Salt Lake City, UT, Mar 5-8, 2015.
11) S.B. Kodandaramaiah, F. Flores, G. Holst, I. Wickersham, E. Brown, C.R. Forest, E.B. Boyden, The Multipatcher: A Robot for High Density Measurement of Intracellular Recordings In Vivo, Proceedings of the Biomedical Engineering Society (BMES) 2014, San Antonio, TX, Oct 22-25, 2014.
12) I. Kolb*, G. Holst*, S.B. Kodandaramaiah, W. Stoy, E.S. Boyden, C.R. Forest. Linear Micro-Actuation System for Patch-Clamp Recording. Proceedings of the 29th Annual Meeting of the American Society for Precision Engineering. Boston, MA.
13) J. Go, A. Fan, C. Lu, S. B. Kodandaramaiah, G. L. Holst, W. Stoy, I. Kolb, E. S. Boyden, C. R. Forest, Fully-automated in vivo single cell electrophysiology, Proceedings of the 28th Annual Meeting of the American Society for Precision Engineering 2013, St. Paul, MN, October 20-October 55, 2013
14) I. Kolb, G. B. Holst, B. Goldstein, S.B. Kodandaramaiah, E.S. Boyden, E. Culurciello, C.R. Forest, Automated, in-vivo, whole-cell electrophysiology using an integrated patch-clamp amplifier, Proceedings of the 22nd Annual Computational Neuroscience Meeting (CNS 2013), Paris, France, July 13-18, 2013.
15) S. B. Kodandaramaiah, A. S. Chuong, M. Ogawa, N. Klapoetke, M. Baratta, L. C. Acker, P. E. Monahan, F. Yoshida, E. S. Boyden, and C. R. Forest, Integration of automated patch clamp electrophysiology system with optogenetics for cell type identification in vivo, Proceedings of the Annual Meeting of the Biomedical Engineering Society (BMES) 2012, Atlanta, GA, October 24-27, 2012
16) D. Chiyo, S. B. Kodandaramaiah, K. Grosh, Z. D. Ma, B. Raju, F. R. Abadi, Reactive Structure and Smart Armor for Army’s Future Ground Vehicles, Proceedings of 25th Annual Army Sciences Conference (ASC 2010), Orlando, Florida, November 29 - December 2, 2010.
17) S. B. Kodandaramaiah, S. Malik, C. R. Forest, Design and performance of telescoping micropipette arrays for high-throughput in vivo patch clamping, Proceedings of the 25th Annual Meeting of the American Society for Precision Engineering, Atlanta, GA, October 31-November 5, 2010, Awarded R.V. Jones Memorial Award for Best Student Paper.
18) N. Pak, C.R. Phaneuf, S. B. Kodandaramaiah, and C.R. Forest, Modulation of electromagnetic radiation using a dot matrix printer, Proceedings of the 25th Annual Meeting of the American Society for Precision Engineering 2010, Atlanta, GA, October 31-November 5, 2010
19) S. B. Kodandaramaiah, N. Chronis, An Opto-fluidic sensor for monitoring Intra-cranial pressure (ICP), Proceedings of the 12th International Conference on micro-Total Analysis Systems, San Diego, CA, October 2008.
20) J. Gregory, Y.S. Ng, E.M. Jung, S. B. Kodandaramaiah, Dielectrophoretic whole blood separation device integrating a spiral pump and cytometry, Proceedings of the 6th IEEE Sensors Conference, Atlanta, GA, October 2007.