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Author Title Type [ Year(Asc)]
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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.
Pachitariu M, Zhong L, Gracias A, Minisi A, Lopez C, Stringer C.  2025.  A critical initialization for biological neural networks. 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.
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.
2021
Stringer C, Wang T, Michaelos M, Pachitariu M.  2021.  Cellpose: a generalist algorithm for cellular segmentation.. Nature Methods. 18(1):100-106.
Stringer C, Michaelos M, Tsyboulski D, Lindo SE, Pachitariu M.  2021.  High-precision coding in visual cortex.. Cell. 184(10):2767-78.
2020
Stringer C, Michaelos M, Pachitariu M.  2020.  Cellpose: a generalist algorithm for cellular segmentation. bioRxiv.
2019
Stringer C, Michaelos M, Pachitariu M.  2019.  High precision coding in visual cortex. BioRxiv. :679324.
Stringer C, Pachitariu M, Steinmetz NA, Carandini M, Harris KD.  2019.  High-dimensional geometry of population responses in visual cortex.. Nature. 571(7765):361-65.
Stringer C, Pachitariu M, Steinmetz NA, Reddy CBai, Carandini M, Harris KD.  2019.  Spontaneous behaviors drive multidimensional, brain-wide population activity.. Science. 364(6437):255.