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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: Network States Classification based on Local Field Potential Recordings in the Awake Mouse Neocortex.

Zerlaut, Yann / Zucca, Stefano / Fellin, Tommaso / Panzeri, Stefano

eNeuro

2022 Volume 9, Issue 4

Abstract: Recent studies using intracellular recordings in awake behaving mice revealed that cortical network states, defined based on membrane potential features, modulate sensory responses and perceptual outcomes. Single-cell intracellular recordings are ... ...

Abstract	Recent studies using intracellular recordings in awake behaving mice revealed that cortical network states, defined based on membrane potential features, modulate sensory responses and perceptual outcomes. Single-cell intracellular recordings are difficult and have low yield compared to extracellular recordings of population signals, such as local field potentials (LFPs). However, it is currently unclear how to identify these behaviorally-relevant network states from the LFP. We used simultaneous LFP and intracellular recordings in the somatosensory cortex of awake mice to design a network state classification from the LFP, the Network State Index (NSI). We used the NSI to analyze the relationship between single-cell (intracellular) and population (LFP) signals over different network states of wakefulness. We found that graded levels of population signal faithfully predicted the levels of single-cell depolarization in nonrhythmic regimes whereas, in δ ([2-4 Hz]) oscillatory regimes, the graded levels of rhythmicity in the LFP mapped into a stereotypical oscillatory pattern of membrane potential. Finally, we showed that the variability of network states, beyond the occurrence of slow oscillatory activity, critically shaped the average correlations between single-cell and population signals. Application of the LFP-based NSI to mouse visual cortex data showed that this index increased with pupil size and during locomotion and had a U-shaped dependence on population firing rates. NSI-based characterization provides a ready-to-use tool to understand from LFP recordings how the modulation of local network dynamics shapes the flexibility of sensory processing during behavior.
MeSH term(s)	Action Potentials/physiology ; Animals ; Membrane Potentials/physiology ; Mice ; Neocortex ; Neurons/physiology ; Visual Cortex/physiology ; Wakefulness/physiology
Language	English
Publishing date	2022-08-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	2800598-3
ISSN	2373-2822 ; 2373-2822
ISSN (online)	2373-2822
ISSN	2373-2822
DOI	10.1523/ENEURO.0073-22.2022
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Article: SmaRT2P: a software for generating and processing smart line recording trajectories for population two-photon calcium imaging.

Moroni, Monica / Brondi, Marco / Fellin, Tommaso / Panzeri, Stefano

Brain informatics

2022 Volume 9, Issue 1, Page(s) 18

Abstract: Two-photon fluorescence calcium imaging allows recording the activity of large neural populations with subcellular spatial resolution, but it is typically characterized by low signal-to-noise ratio (SNR) and poor accuracy in detecting single or few ... ...

Abstract	Two-photon fluorescence calcium imaging allows recording the activity of large neural populations with subcellular spatial resolution, but it is typically characterized by low signal-to-noise ratio (SNR) and poor accuracy in detecting single or few action potentials when large number of neurons are imaged. We recently showed that implementing a smart line scanning approach using trajectories that optimally sample the regions of interest increases both the SNR fluorescence signals and the accuracy of single spike detection in population imaging in vivo. However, smart line scanning requires highly specialised software to design recording trajectories, interface with acquisition hardware, and efficiently process acquired data. Furthermore, smart line scanning needs optimized strategies to cope with movement artefacts and neuropil contamination. Here, we develop and validate SmaRT2P, an open-source, user-friendly and easy-to-interface Matlab-based software environment to perform optimized smart line scanning in two-photon calcium imaging experiments. SmaRT2P is designed to interface with popular acquisition software (e.g., ScanImage) and implements novel strategies to detect motion artefacts, estimate neuropil contamination, and minimize their impact on functional signals extracted from neuronal population imaging. SmaRT2P is structured in a modular way to allow flexibility in the processing pipeline, requiring minimal user intervention in parameter setting. The use of SmaRT2P for smart line scanning has the potential to facilitate the functional investigation of large neuronal populations with increased SNR and accuracy in detecting the discharge of single and few action potentials.
Language	English
Publishing date	2022-08-04
Publishing country	Germany
Document type	Journal Article
ISSN	2198-4018
ISSN	2198-4018
DOI	10.1186/s40708-022-00166-4
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Article ; Online: SmaRT2P

Monica Moroni / Marco Brondi / Tommaso Fellin / Stefano Panzeri

Brain Informatics, Vol 9, Iss 1, Pp 1-

a software for generating and processing smart line recording trajectories for population two-photon calcium imaging

2022 Volume 19

Abstract: Abstract Two-photon fluorescence calcium imaging allows recording the activity of large neural populations with subcellular spatial resolution, but it is typically characterized by low signal-to-noise ratio (SNR) and poor accuracy in detecting single or ... ...

Abstract	Abstract Two-photon fluorescence calcium imaging allows recording the activity of large neural populations with subcellular spatial resolution, but it is typically characterized by low signal-to-noise ratio (SNR) and poor accuracy in detecting single or few action potentials when large number of neurons are imaged. We recently showed that implementing a smart line scanning approach using trajectories that optimally sample the regions of interest increases both the SNR fluorescence signals and the accuracy of single spike detection in population imaging in vivo. However, smart line scanning requires highly specialised software to design recording trajectories, interface with acquisition hardware, and efficiently process acquired data. Furthermore, smart line scanning needs optimized strategies to cope with movement artefacts and neuropil contamination. Here, we develop and validate SmaRT2P, an open-source, user-friendly and easy-to-interface Matlab-based software environment to perform optimized smart line scanning in two-photon calcium imaging experiments. SmaRT2P is designed to interface with popular acquisition software (e.g., ScanImage) and implements novel strategies to detect motion artefacts, estimate neuropil contamination, and minimize their impact on functional signals extracted from neuronal population imaging. SmaRT2P is structured in a modular way to allow flexibility in the processing pipeline, requiring minimal user intervention in parameter setting. The use of SmaRT2P for smart line scanning has the potential to facilitate the functional investigation of large neuronal populations with increased SNR and accuracy in detecting the discharge of single and few action potentials.
Keywords	Two-photon microscopy ; Line scanning ; Calcium imaging ; Open-source software ; Neuroinformatics ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Computer software ; QA76.75-76.765
Subject code	006
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	SpringerOpen
Document type	Article ; Online
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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: Complementary encoding of spatial information in hippocampal astrocytes

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

PLoS Biology, Vol 20, Iss

2022 Volume 3

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. A combination of functional imaging of astrocytes and neurons in the mouse hippocampus with information theory analysis shows that calcium dynamics in topographically-organized subcellular regions of astrocytes encode information about an animal’s position that is complementary and synergistic to that encoded in the spike output of surrounding neurons.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2022-03-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Optogenetic strategies for high-efficiency all-optical interrogation using blue-light-sensitive opsins.

Forli, Angelo / Pisoni, Matteo / Printz, Yoav / Yizhar, Ofer / Fellin, Tommaso

eLife

2021 Volume 10

Abstract: All-optical methods for imaging and manipulating brain networks with high spatial resolution are fundamental to study how neuronal ensembles drive behavior. Stimulation of neuronal ensembles using two-photon holographic techniques requires high- ... ...

Abstract	All-optical methods for imaging and manipulating brain networks with high spatial resolution are fundamental to study how neuronal ensembles drive behavior. Stimulation of neuronal ensembles using two-photon holographic techniques requires high-sensitivity actuators to avoid photodamage and heating. Moreover, two-photon-excitable opsins should be insensitive to light at wavelengths used for imaging. To achieve this goal, we developed a novel soma-targeted variant of the large-conductance blue-light-sensitive opsin CoChR (stCoChR). In the mouse cortex in vivo, we combined holographic two-photon stimulation of stCoChR with an amplified laser tuned at the opsin absorption peak and two-photon imaging of the red-shifted indicator jRCaMP1a. Compared to previously characterized blue-light-sensitive soma-targeted opsins in vivo, stCoChR allowed neuronal stimulation with more than 10-fold lower average power and no spectral crosstalk. The combination of stCoChR, tuned amplified laser stimulation, and red-shifted functional indicators promises to be a powerful tool for large-scale interrogation of neural networks in the intact brain.
MeSH term(s)	Animals ; Cerebral Cortex/cytology ; Cerebral Cortex/metabolism ; Cerebral Cortex/radiation effects ; Light ; Mice ; Neurons/radiation effects ; Opsins/metabolism ; Optogenetics ; Photons
Chemical Substances	Opsins
Language	English
Publishing date	2021-05-25
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.63359
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Article ; Online: Stimulus Feature-Specific Control of Layer 2/3 Subthreshold Whisker Responses by Layer 4 in the Mouse Primary Somatosensory Cortex.

Varani, Stefano / Vecchia, Dania / Zucca, Stefano / Forli, Angelo / Fellin, Tommaso

Cerebral cortex (New York, N.Y. : 1991)

2021 Volume 32, Issue 7, Page(s) 1419–1436

Abstract: In the barrel field of the rodent primary somatosensory cortex (S1bf), excitatory cells in layer 2/3 (L2/3) display sparse firing but reliable subthreshold response during whisker stimulation. Subthreshold responses encode specific features of the ... ...

Abstract	In the barrel field of the rodent primary somatosensory cortex (S1bf), excitatory cells in layer 2/3 (L2/3) display sparse firing but reliable subthreshold response during whisker stimulation. Subthreshold responses encode specific features of the sensory stimulus, for example, the direction of whisker deflection. According to the canonical model for the flow of sensory information across cortical layers, activity in L2/3 is driven by layer 4 (L4). However, L2/3 cells receive excitatory inputs from other regions, raising the possibility that L4 partially drives L2/3 during whisker stimulation. To test this hypothesis, we combined patch-clamp recordings from L2/3 pyramidal neurons in S1bf with selective optogenetic inhibition of L4 during passive whisker stimulation in both anesthetized and awake head-restrained mice. We found that L4 optogenetic inhibition did not abolish the subthreshold whisker-evoked response nor it affected spontaneous membrane potential fluctuations of L2/3 neurons. However, L4 optogenetic inhibition decreased L2/3 subthreshold responses to whisker deflections in the preferred direction, and it increased L2/3 responses to stimuli in the nonpreferred direction, leading to a change in the direction tuning. Our results contribute to reveal the circuit mechanisms underlying the processing of sensory information in the rodent S1bf.
MeSH term(s)	Animals ; Membrane Potentials ; Mice ; Neurons/physiology ; Pyramidal Cells/physiology ; Somatosensory Cortex/physiology ; Vibrissae/physiology
Language	English
Publishing date	2021-08-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	1077450-6
ISSN	1460-2199 ; 1047-3211
ISSN (online)	1460-2199
ISSN	1047-3211
DOI	10.1093/cercor/bhab297
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Article ; Online: The Spectrum of Asynchronous Dynamics in Spiking Networks as a Model for the Diversity of Non-rhythmic Waking States in the Neocortex.

Zerlaut, Yann / Zucca, Stefano / Panzeri, Stefano / Fellin, Tommaso

Cell reports

2019 Volume 27, Issue 4, Page(s) 1119–1132.e7

Abstract: The awake cortex exhibits diverse non-rhythmic network states. However, how these states emerge and how each state impacts network function is unclear. Here, we demonstrate that model networks of spiking neurons with moderate recurrent interactions ... ...

Abstract	The awake cortex exhibits diverse non-rhythmic network states. However, how these states emerge and how each state impacts network function is unclear. Here, we demonstrate that model networks of spiking neurons with moderate recurrent interactions display a spectrum of non-rhythmic asynchronous dynamics based on the level of afferent excitation, from afferent input-dominated (AD) regimes, characterized by unbalanced synaptic currents and sparse firing, to recurrent input-dominated (RD) regimes, characterized by balanced synaptic currents and dense firing. The model predicted regime-specific relationships between different neural biophysical properties, which were all experimentally validated in the somatosensory cortex (S1) of awake mice. Moreover, AD regimes more precisely encoded spatiotemporal patterns of presynaptic activity, while RD regimes better encoded the strength of afferent inputs. These results provide a theoretical foundation for how recurrent neocortical circuits generate non-rhythmic waking states and how these different states modulate the processing of incoming information.
MeSH term(s)	Action Potentials ; Models, Neurological ; Neocortex/physiology ; Nerve Net/physiology ; Neurons/physiology ; Somatosensory Cortex/physiology ; Synaptic Transmission/physiology ; Wakefulness
Language	English
Publishing date	2019-04-23
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2019.03.102
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Article ; Online: Optogenetic strategies for high-efficiency all-optical interrogation using blue-light-sensitive opsins

Angelo Forli / Matteo Pisoni / Yoav Printz / Ofer Yizhar / Tommaso Fellin

eLife, Vol

2021 Volume 10

Abstract	All-optical methods for imaging and manipulating brain networks with high spatial resolution are fundamental to study how neuronal ensembles drive behavior. Stimulation of neuronal ensembles using two-photon holographic techniques requires high-sensitivity actuators to avoid photodamage and heating. Moreover, two-photon-excitable opsins should be insensitive to light at wavelengths used for imaging. To achieve this goal, we developed a novel soma-targeted variant of the large-conductance blue-light-sensitive opsin CoChR (stCoChR). In the mouse cortex in vivo, we combined holographic two-photon stimulation of stCoChR with an amplified laser tuned at the opsin absorption peak and two-photon imaging of the red-shifted indicator jRCaMP1a. Compared to previously characterized blue-light-sensitive soma-targeted opsins in vivo, stCoChR allowed neuronal stimulation with more than 10-fold lower average power and no spectral crosstalk. The combination of stCoChR, tuned amplified laser stimulation, and red-shifted functional indicators promises to be a powerful tool for large-scale interrogation of neural networks in the intact brain.
Keywords	two-photon optogenetics ; mouse cortex ; soma targeting ; CoChR ; red-shifted functional indicators ; jRCaMP1a ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	535
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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