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Article: ASTRA: a deep learning algorithm for fast semantic segmentation of large-scale astrocytic networks.

Bonato, Jacopo / Curreli, Sebastiano / Romanzi, Sara / Panzeri, Stefano / Fellin, Tommaso

bioRxiv : the preprint server for biology

2023

Abstract: Changes in the intracellular calcium concentration are a fundamental fingerprint of astrocytes, the main type of glial cell. Astrocyte calcium signals can be measured with two-photon microscopy, occur in anatomically restricted subcellular regions, and ... ...

Abstract	Changes in the intracellular calcium concentration are a fundamental fingerprint of astrocytes, the main type of glial cell. Astrocyte calcium signals can be measured with two-photon microscopy, occur in anatomically restricted subcellular regions, and are coordinated across astrocytic networks. However, current analytical tools to identify the astrocytic subcellular regions where calcium signals occur are time-consuming and extensively rely on user-defined parameters. These limitations limit reproducibility and prevent scalability to large datasets and fields-of-view. Here, we present Astrocytic calcium Spatio-Temporal Rapid Analysis (ASTRA), a novel software combining deep learning with image feature engineering for fast and fully automated semantic segmentation of two-photon calcium imaging recordings of astrocytes. We applied ASTRA to several two-photon microscopy datasets and found that ASTRA performed rapid detection and segmentation of astrocytic cell somata and processes with performance close to that of human experts, outperformed state-of-the-art algorithms for the analysis of astrocytic and neuronal calcium data, and generalized across indicators and acquisition parameters. We also applied ASTRA to the first report of two-photon mesoscopic imaging of hundreds of astrocytes in awake mice, documenting large-scale redundant and synergistic interactions in extended astrocytic networks. ASTRA is a powerful tool enabling closed-loop and large-scale reproducible investigation of astrocytic morphology and function.
Language	English
Publishing date	2023-05-03
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.05.03.539211
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Article ; Online: Complementary encoding of spatial information in hippocampal astrocytes.

Curreli, Sebastiano / Bonato, Jacopo / Romanzi, Sara / Panzeri, Stefano / Fellin, Tommaso

PLoS biology

2022 Volume 20, Issue 3, Page(s) e3001530

Abstract: Calcium dynamics into astrocytes influence the activity of nearby neuronal structures. However, because previous reports show that astrocytic calcium signals largely mirror neighboring neuronal activity, current information coding models neglect ... ...

Abstract	Calcium dynamics into astrocytes influence the activity of nearby neuronal structures. However, because previous reports show that astrocytic calcium signals largely mirror neighboring neuronal activity, current information coding models neglect astrocytes. Using simultaneous two-photon calcium imaging of astrocytes and neurons in the hippocampus of mice navigating a virtual environment, we demonstrate that astrocytic calcium signals encode (i.e., statistically reflect) spatial information that could not be explained by visual cue information. Calcium events carrying spatial information occurred in topographically organized astrocytic subregions. Importantly, astrocytes encoded spatial information that was complementary and synergistic to that carried by neurons, improving spatial position decoding when astrocytic signals were considered alongside neuronal ones. These results suggest that the complementary place dependence of localized astrocytic calcium signals may regulate clusters of nearby synapses, enabling dynamic, context-dependent variations in population coding within brain circuits.
MeSH term(s)	Algorithms ; Animals ; Astrocytes/cytology ; Astrocytes/metabolism ; CA1 Region, Hippocampal/cytology ; CA1 Region, Hippocampal/metabolism ; Calcium/metabolism ; Calcium Signaling/physiology ; Locomotion/physiology ; Male ; Mice, Inbred C57BL ; Models, Neurological ; Neurons/cytology ; Neurons/metabolism ; Spatial Navigation/physiology ; Synapses/metabolism ; Synapses/physiology ; Visual Perception/physiology ; Mice
Chemical Substances	Calcium (SY7Q814VUP)
Language	English
Publishing date	2022-03-03
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.3001530
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Article ; Online: A deep-learning approach for online cell identification and trace extraction in functional two-photon calcium imaging.

Sità, Luca / Brondi, Marco / Lagomarsino de Leon Roig, Pedro / Curreli, Sebastiano / Panniello, Mariangela / Vecchia, Dania / Fellin, Tommaso

Nature communications

2022 Volume 13, Issue 1, Page(s) 1529

Abstract: In vivo two-photon calcium imaging is a powerful approach in neuroscience. However, processing two-photon calcium imaging data is computationally intensive and time-consuming, making online frame-by-frame analysis challenging. This is especially true for ...

Abstract	In vivo two-photon calcium imaging is a powerful approach in neuroscience. However, processing two-photon calcium imaging data is computationally intensive and time-consuming, making online frame-by-frame analysis challenging. This is especially true for large field-of-view (FOV) imaging. Here, we present CITE-On (Cell Identification and Trace Extraction Online), a convolutional neural network-based algorithm for fast automatic cell identification, segmentation, identity tracking, and trace extraction in two-photon calcium imaging data. CITE-On processes thousands of cells online, including during mesoscopic two-photon imaging, and extracts functional measurements from most neurons in the FOV. Applied to publicly available datasets, the offline version of CITE-On achieves performance similar to that of state-of-the-art methods for offline analysis. Moreover, CITE-On generalizes across calcium indicators, brain regions, and acquisition parameters in anesthetized and awake head-fixed mice. CITE-On represents a powerful tool to speed up image analysis and facilitate closed-loop approaches, for example in combined all-optical imaging and manipulation experiments.
MeSH term(s)	Algorithms ; Animals ; Calcium ; Deep Learning ; Image Processing, Computer-Assisted/methods ; Mice ; Neural Networks, Computer
Chemical Substances	Calcium (SY7Q814VUP)
Language	English
Publishing date	2022-03-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-29180-0
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Article ; Online: Extracellular matrix alterations in the ketamine model of schizophrenia.

Matuszko, Gabriela / Curreli, Sebastiano / Kaushik, Rahul / Becker, Axel / Dityatev, Alexander

Neuroscience

2017 Volume 350, Page(s) 13–22

Abstract: The neural extracellular matrix (ECM) plays an important role in regulation of perisomatic GABAergic inhibition and synaptic plasticity in the hippocampus and cortex. Decreased labeling of perineuronal nets, a form of ECM predominantly associated with ... ...

Abstract	The neural extracellular matrix (ECM) plays an important role in regulation of perisomatic GABAergic inhibition and synaptic plasticity in the hippocampus and cortex. Decreased labeling of perineuronal nets, a form of ECM predominantly associated with parvalbumin-expressing interneurons in the brain, has been observed in post-mortem studies of schizophrenia patients, specifically, in brain areas such as prefrontal cortex, entorhinal cortex, and amygdala. Moreover, glial ECM in the form of dandelion clock-like structures was reported to be altered in schizophrenia patients. Here, we verified whether similar abnormalities in neural ECM can be reproduced in a rat model of schizophrenia, in which animals received sub-chronic administration of ketamine to reproduce the aspects of disease related to disrupted signaling through N-methyl-D-aspartate receptors. Our study focused on two schizophrenia-related brain areas, namely the medial prefrontal cortex (mPFC) and hippocampus. Semi-quantitative immunohistochemistry was performed to evaluate investigate ECM expression using Wisteria floribunda agglutinin (WFA) and CS56 antibody, both labeling distinct chondroitin sulfate epitopes enriched in perineuronal nets and glial ECM, respectively. Our analysis revealed that ketamine-treated rats exhibit reduced number of WFA-labeled perineuronal nets, and a decreased intensity of parvalbumin fluorescence in mPFC interneurons somata. Moreover, we found an increased expression of CS56 immunoreactive form of ECM. Importantly, the loss of perineuronal nets was revealed in the mPFC, and was not detected in the hippocampus, suggesting regional specificity of ECM alterations. These data open an avenue for further investigations of functional importance of ECM abnormalities in schizophrenia as well as for search of treatments for their compensation.
MeSH term(s)	Amygdala/drug effects ; Amygdala/metabolism ; Animals ; Disease Models, Animal ; Extracellular Matrix/drug effects ; Extracellular Matrix/metabolism ; Hippocampus/drug effects ; Hippocampus/metabolism ; Immunohistochemistry/methods ; Ketamine/pharmacology ; Male ; Neuroglia/drug effects ; Neuroglia/metabolism ; Neurons/drug effects ; Neurons/metabolism ; Parvalbumins/metabolism ; Rats, Sprague-Dawley ; Schizophrenia/chemically induced ; Schizophrenia/metabolism
Chemical Substances	Parvalbumins ; Ketamine (690G0D6V8H)
Language	English
Publishing date	2017-03-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	196739-3
ISSN	1873-7544 ; 0306-4522
ISSN (online)	1873-7544
ISSN	0306-4522
DOI	10.1016/j.neuroscience.2017.03.010
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Zs.A 1215: Show issues

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Article ; Online: Sensitive multicolor indicators for monitoring norepinephrine in vivo.

Nature methods

2023 Volume 20, Issue 9, Page(s) 1426–1436

Abstract: Genetically encoded indicators engineered from G-protein-coupled receptors are important tools that enable high-resolution in vivo neuromodulator imaging. Here, we introduce a family of sensitive multicolor norepinephrine (NE) indicators, which includes ... ...

Abstract	Genetically encoded indicators engineered from G-protein-coupled receptors are important tools that enable high-resolution in vivo neuromodulator imaging. Here, we introduce a family of sensitive multicolor norepinephrine (NE) indicators, which includes nLightG (green) and nLightR (red). These tools report endogenous NE release in vitro, ex vivo and in vivo with improved sensitivity, ligand selectivity and kinetics, as well as a distinct pharmacological profile compared with previous state-of-the-art GRAB
MeSH term(s)	Animals ; Mice ; Norepinephrine ; Locus Coeruleus/physiology ; Hippocampus/physiology ; Receptors, G-Protein-Coupled
Chemical Substances	Norepinephrine (X4W3ENH1CV) ; Receptors, G-Protein-Coupled
Language	English
Publishing date	2023-07-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2169522-2
ISSN	1548-7105 ; 1548-7091
ISSN (online)	1548-7105
ISSN	1548-7091
DOI	10.1038/s41592-023-01959-z
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Conference proceedings ; Online: TERRITORIAL INTEGRATION AND MARINAS IN SARDINIA

Curreli, Sebastiano / Pira, Cheti

2011

Abstract: Nautical tourism, considered one of the elect expressions of Italy's offer in the field of tourism, assumes new strategic importance in Sardinia's economic and social framework in the light of the fallout it generates in terms of development and the ... ...

Abstract	Nautical tourism, considered one of the elect expressions of Italy's offer in the field of tourism, assumes new strategic importance in Sardinia's economic and social framework in the light of the fallout it generates in terms of development and the multifaceted composition of the demand which today characterizes the sector. Such considerations are confirmed by the incidence of the fleet of pleasure craft compared to the resident population, although paradoxically the important marinas are present in areas that are marginal in the panorama of the region's holiday industry. This fact emphasizes the lack of correspondence between an important number of infrastructures - Sardinia is the second Italian region for port infrastructures and berths - and effective territorial integration between nautical installations and inland holiday resort structures. This is to say that it is still quite difficult to interpret the territorial effects of marinas on accommodation facilities.
Keywords	ddc:330
Subject code	910
Language	English
Publisher	Louvain-la-Neuve: European Regional Science Association (ERSA)
Publishing country	de
Document type	Conference proceedings ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Role of Btg2 in the progression of a PDGF-induced oligodendroglioma model.

Appolloni, Irene / Curreli, Sebastiano / Caviglia, Sara / Barilari, Manuela / Gambini, Eleonora / Pagano, Aldo / Malatesta, Paolo

International journal of molecular sciences

2012 Volume 13, Issue 11, Page(s) 14667–14678

Abstract: Tumor progression is a key aspect in oncology. Not even the overexpression of a powerful oncogenic stimulus such as platelet derived growth factor-B (PDGF-B) is sufficient per se to confer full malignancy to cells. In previous studies we showed that ... ...

Abstract	Tumor progression is a key aspect in oncology. Not even the overexpression of a powerful oncogenic stimulus such as platelet derived growth factor-B (PDGF-B) is sufficient per se to confer full malignancy to cells. In previous studies we showed that neural progenitors overexpressing PDGF-B need to undergo progression to acquire the capability to give rise to secondary tumor following transplant. By comparing the expression profile of PDGF-expressing cells before and after progression, we found that progressed tumors consistently downregulate the expression of the antiproliferative gene Btg2. We therefore tested whether the downregulation of Btg2 is sufficient and necessary for glioma progression with loss and gain of function experiments. Our results show that downregulation of Btg2 is not sufficient but is necessary for tumor progression since the re-introduction of Btg2 in fully progressed tumors dramatically impairs their gliomagenic potential. These results suggest an important role of Btg2 in glioma progression. Accordingly with this view, the analysis of public datasets of human gliomas showed that reduced level of Btg2 expression correlates with a significantly worse prognosis.
MeSH term(s)	Animals ; Brain Neoplasms/genetics ; Brain Neoplasms/metabolism ; Brain Neoplasms/mortality ; Brain Neoplasms/pathology ; Cell Line ; Cell Transformation, Neoplastic/genetics ; Cell Transformation, Neoplastic/metabolism ; Disease Models, Animal ; Disease Progression ; Down-Regulation ; Female ; Gene Expression Regulation, Neoplastic ; Humans ; Immediate-Early Proteins/genetics ; Immediate-Early Proteins/metabolism ; Mice ; Neoplasm Grading ; Oligodendroglioma/genetics ; Oligodendroglioma/metabolism ; Oligodendroglioma/mortality ; Oligodendroglioma/pathology ; Protein Binding ; Proto-Oncogene Proteins c-sis/genetics ; Proto-Oncogene Proteins c-sis/metabolism ; RNA Interference ; Transduction, Genetic ; Tumor Suppressor Protein p53/genetics ; Tumor Suppressor Protein p53/metabolism ; Tumor Suppressor Proteins/genetics ; Tumor Suppressor Proteins/metabolism
Chemical Substances	Immediate-Early Proteins ; Proto-Oncogene Proteins c-sis ; Tumor Suppressor Protein p53 ; Tumor Suppressor Proteins ; BTG2 protein, human (141490-22-4)
Language	English
Publishing date	2012-11-12
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms131114667
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Article: Rapid generation of functional dopaminergic neurons from human induced pluripotent stem cells through a single-step procedure using cell lineage transcription factors.

Theka, Ilda / Caiazzo, Massimiliano / Dvoretskova, Elena / Leo, Damiana / Ungaro, Federica / Curreli, Sebastiano / Managò, Francesca / Dell'Anno, Maria Teresa / Pezzoli, Gianni / Gainetdinov, Raul R / Dityatev, Alexander / Broccoli, Vania

Stem cells translational medicine

2013 Volume 2, Issue 6, Page(s) 473–479

Abstract: Current protocols for in vitro differentiation of human induced pluripotent stem cells (hiPSCs) to generate dopamine (DA) neurons are laborious and time-expensive. In order to accelerate the overall process, we have established a fast protocol by ... ...

Abstract	Current protocols for in vitro differentiation of human induced pluripotent stem cells (hiPSCs) to generate dopamine (DA) neurons are laborious and time-expensive. In order to accelerate the overall process, we have established a fast protocol by expressing the developmental transcription factors ASCL1, NURR1, and LMX1A. With this method, we were able to generate mature and functional dopaminergic neurons in as few as 21 days, skipping all the intermediate steps for inducting and selecting embryoid bodies and rosette-neural precursors. Strikingly, the resulting neuronal conversion process was very proficient, with an overall efficiency that was more than 93% of all the coinfected cells. hiPSC-derived DA neurons expressed all the critical molecular markers of the DA molecular machinery and exhibited sophisticated functional features including spontaneous electrical activity and dopamine release. This one-step protocol holds important implications for in vitro disease modeling and is particularly amenable for exploitation in high-throughput screening protocols.
MeSH term(s)	Basic Helix-Loop-Helix Transcription Factors/genetics ; Basic Helix-Loop-Helix Transcription Factors/metabolism ; Biomarkers/metabolism ; Cell Differentiation ; Cell Lineage/physiology ; Cells, Cultured ; Dopamine/metabolism ; Dopaminergic Neurons/cytology ; Dopaminergic Neurons/physiology ; Gene Expression Regulation, Developmental ; Genetic Vectors ; Humans ; Induced Pluripotent Stem Cells/cytology ; Induced Pluripotent Stem Cells/physiology ; LIM-Homeodomain Proteins/genetics ; LIM-Homeodomain Proteins/metabolism ; Lentivirus/genetics ; Membrane Potentials/physiology ; Nuclear Receptor Subfamily 4, Group A, Member 2/genetics ; Nuclear Receptor Subfamily 4, Group A, Member 2/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Tubulin/genetics ; Tubulin/metabolism
Chemical Substances	ASCL1 protein, human ; Basic Helix-Loop-Helix Transcription Factors ; Biomarkers ; LIM-Homeodomain Proteins ; LMX1A protein, human ; NR4A2 protein, human ; Nuclear Receptor Subfamily 4, Group A, Member 2 ; TUBB3 protein, human ; Transcription Factors ; Tubulin ; Dopamine (VTD58H1Z2X)
Language	English
Publishing date	2013-05-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2642270-0
ISSN	2157-6580 ; 2157-6564
ISSN (online)	2157-6580
ISSN	2157-6564
DOI	10.5966/sctm.2012-0133
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Article: ASTRA: a deep learning algorithm for fast semantic segmentation of large-scale astrocytic networks.

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Article ; Online: Complementary encoding of spatial information in hippocampal astrocytes.

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Article ; Online: A deep-learning approach for online cell identification and trace extraction in functional two-photon calcium imaging.

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Article ; Online: Extracellular matrix alterations in the ketamine model of schizophrenia.

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Article ; Online: Sensitive multicolor indicators for monitoring norepinephrine in vivo.

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Conference proceedings ; Online: TERRITORIAL INTEGRATION AND MARINAS IN SARDINIA

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Article ; Online: Role of Btg2 in the progression of a PDGF-induced oligodendroglioma model.

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Article: Rapid generation of functional dopaminergic neurons from human induced pluripotent stem cells through a single-step procedure using cell lineage transcription factors.

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