Biblio

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Author Title Type [ Year(Asc)]
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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.
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.
Legorreta EMarquez, Fleishman GM, Hesselink LW, Eddison M, Smeets K, Stringer C, Keller PJ, Narayan S, Chen AB, Mensh BD et al..  2026.  Whole-brain co-mapping of gene expression and neuronal activity at cellular resolution in behaving zebrafish. bioRxiv.
2025
Sun Y, Squires JR, Hoffmann A, Zhang Y, Minor A, Singh A, Scholten D, Mao C, Luo Y, Fang D et al..  2025.  Abstract 2420: Deep learning enables automated detection of circulating tumor cell-immune cell interactions with prognostic insights in cancer. Cancer Research. 85:2420-2420.
Squires JR, Sun Y, Hoffmann AD, Zhang Y, Minor AC, Singh A, Scholten D, Ding H, Mao C, Platanias LC et al..  2025.  Abstract B049: Deep learning enables identification of cell types and clusters (iCTC) in immune tumor ecosystems for prognostic assessment in cancer. Clinical Cancer Research. 31:B049-B049.
Liu H, Squires J, Sun Y, Hoffmann ADaniel, Zhang Y, Platanias LC, Gradishar WJohn, Cristofanilli M, Stringer C.  2025.  Analysis of deep learning for automated recognition of immune cells interacting with CTCs for prognostic assessment in cancer.. Journal of Clinical Oncology. 43:e13028-e13028.
Jacob LPL, Bailes SM, Williams SD, Stringer C, Lewis LD.  2025.  Brainwide hemodynamics predict EEG neural rhythms across sleep and wakefulness in humans.. PLoS Comput Biol. 21(9):e1013497.
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.
Gandin V, Kim J, Yang L-Z, Lian Y, Kawase T, Hu A, Rokicki K, Fleishman G, Tillberg P, Castrejon AAguilera et al..  2025.  Deep-tissue transcriptomics and subcellular imaging at high spatial resolution. Science.
Jacob LPL, Bailes SM, Stringer C, Polimeni JR, Lewis LD.  2025.  Functional MRI signals as fast as 1Hz are coupled to brain states and predict spontaneous neural activity. bioRxiv.
Sun W, Winnubst J, Natrajan M, Lai C, Kajikawa K, Michaelos M, Gattoni R, Stringer C, Flickinger D, Fitzgerald JE et al..  2025.  Learning produces an orthogonalized state machine in the hippocampus.. Nature. 640
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.
Qian X, Coleman K, Jiang S, Kriz AJ, Marciano JH, Luo C, Cai C, Manam MDevi, Caglayan E, Otani A et al..  2025.  Spatial transcriptomics reveals human cortical layer and area specification. Nature.
2024
Stringer C, Pachitariu M.  2024.  Analysis methods for large-scale neuronal recordings.. Science. 386(6722):eadp7429.
Farrants H, Shuai Y, Lemon WC, Hernandez CMonroy, Zhang D, Yang S, Patel R, Qiao G, Frei MS, Plutkis SE et al..  2024.  A modular chemigenetic calcium indicator for multiplexed in vivo functional imaging.. Nat Methods.
Pachitariu M, Sridhar S, Pennington J, Stringer C.  2024.  Spike sorting with Kilosort4. Nat Methods.
2023
Lovelace JW, Ma J, Yadav S, Chhabria K, Shen H, Pang Z, Qi T, Sehgal R, Zhang Y, Bali T et al..  2023.  Vagal sensory neurons mediate the Bezold-Jarisch reflex and induce syncope.. Nature. 623(7986):387-396.
2022
Pachitariu M, Stringer C.  2022.  Cellpose 2.0: how to train your own model.. Nature Methods. 19(12):1634-41.
Avitan L, Stringer C.  2022.  Not so spontaneous: Multi-dimensional representations of behaviors and context in sensory areas.. Neuron. 110(19):3064.
Cutler KJ, Stringer C, Lo TW, Rappez L, Stroustrup N, S Peterson B, Wiggins PA, Mougous JD.  2022.  Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation.. Nature Methods.