GuPPy, a Python toolbox for the analysis of fiber photometry data

Sherathiya, Venus N; Schaid, Michael D.; Seiler, Jillian L.; Lopez, Gabriela C; Lerner, Talia N.

doi:10.1101/2021.07.15.452555

Cited by 6 publications

(7 citation statements)

References 14 publications

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“…GuPPY, another open source fiber photometry tool, remedied a few of the aforementioned issues that were encountered with pMAT (Sherathiya et al, 2021). GuPPY was created in python, making it a true free and open source tool for fiber photometry analysis.…”

Section: Discussionmentioning

confidence: 99%

Pyfiber: an open source python library that facilitates the merge of operant behavior and fiber photometry- focus on intravenous self-administration

Conlisk

Ceau

Fiancette

et al. 2022

Preprint

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Background- Advances in in vivo fluorescent imaging have exploded with the recent developments of genetically encoded calcium indicators (GECIs) and fluorescent biosensors. Their use with a bulk imaging technique such as fiber photometry (FP) can be highly beneficial in identifying neuronal signatures in behavioral neuroscience experiments. Popularity of FP has grown rapidly. Initially applied to classical conditioning, its integration into operant behavior paradigms is progressing. However, in operant behavior, protocols can be complex including numerous scheduled events, while behavioral responses can occur in diverse and non-predictable manners. To optimize data processing and analysis, there is a need for a flexible tool to extract and relate behavioral and fiber photometry data occurring over operant sessions. New Method- Applied to cocaine intravenous self-administration (using ImetronicR polymodal apparati) and FP recordings in the prelimbic cortex (using Doric Lenses photometry system) in the rat, we established Pyfiber, an outline and open source data analysis python library that facilitates the merge of fiber photometry (using Doric Lenses) with operant behavior (using ImetronicR). It allows relating activity changes within a neuronal population to the various behavioral responses and events occurring during operant behavior. Results- We show some of the possibilities and benefits of the analytical tool Pyfiber, which helps to: 1. Extract the different types of events that occur in an operant session, 2. Extract and process the fiber photometry signals, 3. Select events of interest and align them to the corresponding fiber photometry signals, 4. Apply the most appropriate type of FP signal normalization and signal analysis according to the studied type of event or behavioral response, 5. Run data extraction and analysis on multiple individuals and sessions at the same time, 6. Collect results in an easily readable format for statistical analysis. From our data and through the use of Pyfiber, we show that we can successfully record and easily analyze calcium transients surrounding events occurring during a cocaine self-administration paradigm in the rat. Comparison with Existing Method(s)- While other analytical tools can be used for streamlined fiber photometry analysis, they are either too rigid and specific or too flexible, requiring extensive coding to properly fit the data sets. Additionally, current tools do not permit easy exploration of multiple types of events in parallel- something that is possible with Pyfiber. Conclusions- This work established an open source resource that facilitates the pairing of fiber photometry recordings (using Doric Lenses photometry system) with operant behavior (using ImetronicR polymodal apparati), setting a solid foundation in analyzing the relationship between different dimensions of operant behavior with fluorescent signals from brain regions of interest.

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Section: Discussionmentioning

confidence: 99%

Pyfiber: an open source python library that facilitates the merge of operant behavior and fiber photometry- focus on intravenous self-administration

Conlisk

Ceau

Fiancette

et al. 2022

Preprint

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“…Raw signals for 473 nm excitation (GCaMP6f) and 405 nm excitation (isosbestic signal) were recorded using Doric Neuroscience Studio software. We used the Guppy software for analysis 69 . After loading the data, we apply an artifact correction criterion consisting on the removal of the first second of the raw data.…”

Section: Methods Detailsmentioning

confidence: 99%

“…We used the Guppy software for analysis 69 . After loading the data, we apply an artifact correction criterion consisting on the removal of the first second of the raw data.…”

Section: Fiberphotometry Data Acquisition and Analysismentioning

confidence: 99%

Corticotropin-releasing hormone signaling from prefrontal cortex to lateral septum supports social novelty preference

León-Reyes

Diaz

Nogueira

et al. 2022

Preprint

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Social preference, the decision to interact with one member of the same species over another, is a key feature of optimizing social interactions. In rodents, social preference relies on both extrinsic factors, such as sex, strain and kinship, and intrinsic ones, such as the memory of previous encounters, which favors interactions with novel compared to familiar animals (social novelty preference). At present, it is unclear which neuronal circuits guide social preferences and whether such circuits promote social interactions with the preferred individuals or suppress interactions with the non- preferred ones. Although both the infra-limbic area of the pre-frontal cortex (ILA) and the lateral septum (LS) have been shown to support social novelty preference, the neuronal circuits and molecular mechanisms by which these brain regions interact to regulate social interactions are unknown. Here, we identify a population of inhibitory neurons in ILA that express the neuropeptide corticotropin releasing hormone (CRH) and project to the rostro-dorsal region of LS (rdLS). Release of CRH from ILA in rdLS during interactions with familiar mice disinhibits rdLS neurons, thereby suppressing interactions with familiar mice and contributing to social novelty preference. We further demonstrate how the maturation of CRH expression during the first two post-natal weeks enables the developmental shift from a preference for littermates in juveniles to a preference for novel mice in adults.

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“…Fiber photometry data was collected throughout the entire time that mice were in the open field. GuPPy, an open-source Python-based photometry data analysis pipeline, was used to determine dLight1.3b transient timepoints (25). A custom MATLAB script was used to calculate dLight1.3b area-under-the-curve (AUC).…”

Section: Methodsmentioning

confidence: 99%

Chronically elevated corticosterone impairs dopaminergic transmission in the dorsomedial striatum by sex-divergent mechanisms

Holloway

Schaid

Lerner

2022

Preprint

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Background: Major depressive disorder (MDD) is a leading cause of disability worldwide. Individuals with MDD exhibit decreased motivation and deficits in reward processing along with chronically elevated levels of the 'stress hormone,' cortisol. However, the mechanistic relationship between chronically elevated cortisol and behavioral deficits in motivation and reward processing remains unclear. Given that women are diagnosed with MDD at twice the rate of men, it is important to understand whether the mechanisms linking chronically elevated cortisol to the symptoms of MDD differ by sex. Methods: We used subcutaneous implants to chronically elevate free plasma corticosterone (rodent homolog of cortisol; 'CORT') in male and female mice and examined changes in behavior and dopamine system function. We used operant training to assay reward-guided motivation and high-performance liquid chromatography to quantify striatal dopamine content. We assessed dopamine transporter (DAT) function using ex vivo slice imaging and in vivo fiber photometry in combination with a fluorescent dopamine sensor, dLight1.3b. We further quantified DAT expression and phosphorylation using western blot. Results: We found that chronic CORT treatment impaired reward-seeking in both sexes. In female but not male mice, CORT treatment reduced dopamine content in the dorsomedial striatum (DMS). In male but not female mice, the function of the dopamine transporter (DAT) was impaired in DMS. Conclusions: Chronic elevation of CORT impairs reward-seeking by impairing dopaminergic transmission in the DMS, but via different mechanisms in male and female mice. A better understanding of these sex-specific mechanisms could lead to new directions in MDD diagnosis and treatment.

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GuPPy, a Python toolbox for the analysis of fiber photometry data

Cited by 6 publications

References 14 publications

Pyfiber: an open source python library that facilitates the merge of operant behavior and fiber photometry- focus on intravenous self-administration

Pyfiber: an open source python library that facilitates the merge of operant behavior and fiber photometry- focus on intravenous self-administration

Corticotropin-releasing hormone signaling from prefrontal cortex to lateral septum supports social novelty preference

Chronically elevated corticosterone impairs dopaminergic transmission in the dorsomedial striatum by sex-divergent mechanisms

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