Biblio

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2026
Pachitariu M, Zhong L, Gracias A, Minisi A, Lopez C, Stringer C.  2026.  A critical initialization for biological neural networks. Nature.
Stringer C, Ki C, DelGrosso N, LaFosse P, Zhang Q, Pachitariu M.  2026.  Extracting large-scale neural activity with Suite2p. bioRxiv.
O’Connell S, Michaels JA, Wang R, Mamidipaka S, Venkatesh M, Aresh N, Pachitariu M, J. Pruszynski A, Sober SJ, Pandarinath C.  2026.  High performance sorting of motor unit action potentials with EMUsort. bioRxiv.
O’Connell S, Michaels JA, Wang R, Mamidipaka S, Venkatesh M, Aresh N, Pachitariu M, J Pruszynski A, Sober SJ, Pandarinath C.  2026.  High performance sorting of motor unit action potentials with EMUsort. eLife.
Núñez-Ochoa MAngel, Du F, Zhong L, Baptista S, Michaelos M, Sohn A, Baruchin L, Schröder S, Stringer C, Pachitariu M.  2026.  Linking neural representations to behavior using generalization. bioRxiv.
Syeda A, Núñez-Ochoa MAngel, Zhong L, Pachitariu M, Stringer C.  2026.  Orofacial behaviors, not eye movements, govern neural activity in mouse visual cortex. bioRxiv.
LaFosse PK, Flickinger D, Jaindl G, Drinnenberg A, Grødem S, Lensjø KK, Ramakrishnan C, Siverts L’A, Zeng H, Tasic B et al..  2026.  Raster photostimulation of large-scale neural populations. bioRxiv.
Muralidharan S, Leng C, Orts L, Trepka E, Zhu S, Panichello M, Jonikaitis D, Pennington J, Pachitariu M, Moore T.  2026.  A System for live sorting of neuronal spiking activity from large-scale recordings. bioRxiv.
2025
Stringer C, Pachitariu M.  2025.  Cellpose3: One-click image restoration for improved cellular segmentation.. Nat Methods.
Pachitariu M, Rariden M, Stringer C.  2025.  Cellpose-SAM: Superhuman generalization for cellular segmentation. bioRxiv.
Keller JA, Kwak IS, Stark AK, Pachitariu M, Branson K, Dudman JT.  2025.  Cortical control of innate behavior from subcortical demonstration. bioRxiv.
Trautmann EM, Hesse JK, Stine GM, Xia R, Zhu S, O'Shea DJ, Karsh B, Colonell J, Lanfranchi FF, Vyas S et al..  2025.  Large-scale high-density brain-wide neural recording in nonhuman primates.. Nat Neurosci.
Du F, Núñez-Ochoa MAngel, Pachitariu M, Stringer C.  2025.  A simplified minimodel of visual cortical neurons. Nat Commun.
Zhang Q, Grødem S, Gracias A, Lensjø KK, Fyhn M, Stringer C, Pachitariu M.  2025.  Spatial predictive coding in visual cortical neurons. bioRxiv.
2024
Stringer C, Pachitariu M.  2024.  Analysis methods for large-scale neuronal recordings.. Science. 386(6722):eadp7429.
Miura Y, Kim J-il, Jurjut O, Kelley KW, Yang X, Chen X, Thete MVijay, Revah O, Cui B, Pachitariu M et al..  2024.  Assembloid model to study loop circuits of the human nervous system. bioRxiv.
Hoeller J, Zhong L, Pachitariu M, Romani S.  2024.  Bridging tuning and invariance with equivariant neuronal representations. bioRxiv.
Pachitariu M, Sridhar S, Pennington J, Stringer C.  2024.  Spike sorting with Kilosort4. Nat Methods.
2023
Stagkourakis S, Spigolon G, Marks M, Feyder M, Kim J, Perona P, Pachitariu M, Anderson DJ.  2023.  Anatomically distributed neural representations of instincts in the hypothalamus.. bioRxiv.
2022
Pachitariu M, Stringer C.  2022.  Cellpose 2.0: how to train your own model.. Nature Methods. 19(12):1634-41.
Pandey B, Pachitariu M, Brunton BW, Harris KDecker.  2022.  Structured random receptive fields enable informative sensory encodings.. PLoS Computational Biology. 18(10):e1010484.
Gardner RJ, Hermansen E, Pachitariu M, Burak Y, Baas NA, Dunn BA, Moser M-B, Moser EI.  2022.  Toroidal topology of population activity in grid cells.. Nature. 602(7895):123-128.
2021
Stringer C, Wang T, Michaelos M, Pachitariu M.  2021.  Cellpose: a generalist algorithm for cellular segmentation.. Nature Methods. 18(1):100-106.
Lee KHyun, Ni Y-L, Colonell J, Karsh B, Putzeys J, Pachitariu M, Harris TD, Meister M.  2021.  Electrode pooling can boost the yield of extracellular recordings with switchable silicon probes.. Nature Communications. 12(1):5245.
Stringer C, Michaelos M, Tsyboulski D, Lindo SE, Pachitariu M.  2021.  High-precision coding in visual cortex.. Cell. 184(10):2767-78.