Cantin Ortiz

• Signorelli, Letizia; Korchynska, Solomiia; Ortiz, Cantin; Arena, Alessandro; Wilhelm, Sophia Anna & Boccara, Charlotte (2026). Nyx: a flexible framework for sleep scoring across species, lifespan and modalities. bioRxiv - the preprint server for biology. doi: 10.64898/2026.07.24.740558. Full text in Research Archive Show summary

  Abstract Sleep is a key factor in almost every physiological process, yet scoring tools lag behind innovations in basic to clinical research. New automated algorithms are trained on narrow datasets, typically healthy adult mouse or human, and fail to generalise, leaving labs to fall back on slow, laborious, and often poorly reproducible manual scoring. Here we introduce Nyx, an unsupervised framework built on principal component analysis that flexibly clusters epochs into sleep states, akin to how spike-sorting algorithms cluster single-neuron activity. Validated on about 8,000 hours spanning 19 independent datasets, it generalises across species, lifespan, recording modalities, and altered sleep architectures, matching human inter-scorer agreement. Beyond this, Nyx opens new ground for modern sleep research: classifying NREM subtypes in rodents, revealing states that cut across canonical boundaries in non-mammalian species, and enabling real-time, closed-loop manipulation. Distributed as an open-source package with a graphical user interface, Nyx offers an accessible, explainable framework built to scale with the pace of innovation itself.

• Ortiz, Cantin; Allegra, Manuela & Schmidt-Hieber, Christoph (2025). Task engagement differentially drives hippocampal and neocortical neural codes. BioRxiv. ISSN 0362-4331. doi: 10.1101/2025.06.26.661816. Full text in Research Archive
• Gandit, Bérénice; Posani, Lorenzo; Zhang, Chun-Lei; Saha, Soham; Ortiz, Cantin & Allegra, Manuela [Show all 7 contributors for this article] (2024). Transformation of spatial representations along hippocampal circuits. iScience. doi: 10.1016/j.isci.2024.110361. Full text in Research Archive
• Calvigioni, Daniela; Fuzik, Janos; Merre, Pierre Le; Slashcheva, Marina; Jung, Felix & Ortiz, Cantin [Show all 18 contributors for this article] (2023). Esr1+ hypothalamic-habenula neurons shape aversive states. Nature Neuroscience. ISSN 1097-6256. doi: 10.1038/s41593-023-01367-8. Full text in Research Archive
• Lu, Shaina; Ortiz, Cantin; Fürth, Daniel; Fischer, Stephan; Meletis, Konstantinos & Zador, Anthony [Show all 7 contributors for this article] (2021). Assessing the replicability of spatial gene expression using atlas data from the adult mouse brain. PLoS Biology. ISSN 1544-9173. doi: 10.1371/journal.pbio.3001341. Full text in Research Archive
• Zhang, Chun-Lei; Koukouli, Fani; Allegra, Manuela; Ortiz, Cantin; Kao, Hsin-Lun & Maskos, Uwe [Show all 8 contributors for this article] (2021). Inhibitory control of synaptic signals preceding locomotion in mouse frontal cortex. Cell reports. doi: 10.1016/j.celrep.2021.110035. Full text in Research Archive
• Ortiz, Cantin; Carlén, Marie & Meletis, Konstantinos (2021). Spatial Transcriptomics: Molecular Maps of the Mammalian Brain. Annual Review of Neuroscience. ISSN 0147-006X. doi: 10.1146/annurev-neuro-100520-082639. Full text in Research Archive
• Ortiz, Cantin; Navarro, Jose Fernandez; Jurek, Aleksandra; Märtin, Antje; Lundeberg, Joakim & Meletis, Konstantinos (2020). Molecular atlas of the adult mouse brain. Science Advances. doi: 10.1126/sciadv.abb3446. Full text in Research Archive
• Ährlund-Richter, Sofie; Xuan, Yang; Lunteren, Josina Anna van; Kim, Hoseok; Ortiz, Cantin & Dorocic, Iskra Pollak [Show all 8 contributors for this article] (2019). A whole-brain atlas of monosynaptic input targeting four different cell types in the medial prefrontal cortex of the mouse. Nature Neuroscience. ISSN 1097-6256. doi: 10.1038/s41593-019-0354-y. Full text in Research Archive

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• Signorelli, Letizia; Korchynska, Solomiia; Ortiz, Cantin; Arena, Alessandro; Wilhelm, Sophia Anna & Boccara, Charlotte (2026). Sleep scoring with Nyx: a generalisable framework across species, ages and recording Methods. Full text in Research Archive Show summary

  Background and aims: Sleep scoring is essential for the characterisation of sleep architecture and supports most analyses in sleep research, yet it remains a time-consuming task. While automated sleep scoring has the potential to reduce manual workload and inter-rater variability, its adoption remains limited. Most existing tools are tailored to specific datasets, reducing their generalisability, and function as black-box algorithms, limiting interpretability and undermining researchers' trust. To address these challenges, we present Nyx, a generalisable, explainable, and accessible sleep scoring framework, based on Principal Component Analysis (PCA) for transparent feature extraction and flexible stage clustering. We demonstrate its application across species, lifespan, and recording modalities, and release it as an open-source tool with a graphical user interface (GUI) for non-technical users. Methods: Nyx was first validated on rodent polysomnographic (PSG) data from 17 datasets (10 baseline and 7 experimental manipulations; rats and mice; ~7,937 h of recordings). Then generalisation was evaluated across three dimensions: species (rodents, humans and additional species), developmental stage (juvenile, adolescent and adult), and recording modality, including acquisition setup (wired, wireless and telemetric) and signal combinations (electroencephalography (EEG) with electromyography (EMG), EEG with video or accelerometry, and EEG-only). Agreement with human scorers and established automated tools was quantified using Cohen's κ and F1 score. Preliminary evaluation of real-time sleep classification was also conducted to explore the framework's potential for closed-loop applications. Results: Nyx achieved performance comparable to inter-rater human agreement across all rodent baseline and experimental datasets (κ ≥ 0.80, F1 ≥ 0.85). The framework generalised across species and developmental stages, accurately differentiating human sleep stages (4-stage: κ ≥ 0.70, F1 ≥ 0.80; 5-stage: κ ≥ 0.65, F1 ≥ 0.75), while maintaining consistent performance across age groups. Real-time classification performance indicates suitability for closed-loop experimental applications. Conclusions: Nyx provides a reproducible, generalisable and accessible framework for sleep scoring across species, developmental stages and recording modalities. Its transparent architecture based on PCA addresses a key barrier to the adoption of automated scoring approaches. By enabling consistent analysis across diverse datasets and acquisition methods, Nyx facilitates more standardised sleep research and the exploration of cross-species, lifespan and cross-modality insights.

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