Data from: In-vivo analysis of medial perforant path-evoked excitation and inhibition in dentate granule cells
Data files
May 08, 2026 version files 6.68 GB
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CAIM-AP.mat
922.44 MB
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CAIM-Baseline.mat
157.85 MB
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M103.071216.1325pro.mat
887.69 MB
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M234.071117.1642pro.mat
228.41 MB
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PatchData.zip
4.48 GB
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README.md
14.54 KB
Abstract
Across brain regions and species, the dynamics and balance of excitation and inhibition critically determine neuronal firing. The hippocampal dentate gyrus is a brain area thought to be strongly regulated by inhibition. In vivo, it exhibits remarkably sparse activity, a characteristic proposed to underlie computational tasks like pattern separation. Several populations of interneurons mediate strong feedforward as well as feedback inhibition onto granule cells. However, the dynamics of inhibition control granule cell activity in vivo are insufficiently studied. Using two-photon in vivo Ca2+ imaging in mice of either sex, we show that sensory stimulation activates only a small number of dentate gyrus granule cells, while inducing widespread inhibition across the remaining granule cell population. Dual-color imaging of both bulk medial perforant path activity and individual granule cell activity allowed us to probe input–output conversion in this pathway. To examine the interplay of MPP-evoked excitation and inhibition at the cellular level, we used in vivo whole-cell patch-clamp recordings while simultaneously photo-activating MPP inputs. Our findings reveal that MPP-triggered inhibition is fast, significantly larger than excitation, and long-lasting. These results reveal specific properties of inhibition in the dentate gyrus that are likely crucial for its computational functions, in maintaining sparse activity with a high signal-to-noise ratio.
Dataset DOI: 10.5061/dryad.tdz08kqch
Description of the data and file structure
The data were recorded from BL6/C57 mice, and all animal experiments were conducted in accordance with European (2010/63/EU) and federal law (TierSchG, TierSchVersV) on animal care and use and approved by the county of North-Rhine Westphalia (LANUV AZ 84-02.04.2015.A524, AZ 81- 56 02.04.2019.A216). The dataset contains recordings from dentate granule cells in vivo using two different techniques:
- Imaging data have been obtained using two-photon (2P) scanning microscopy in awake animals running on a linear treadmill. The calcium indicator GCaMP6s has been expressed in a subset of all excitatory cells in mouse brains using a Thy1 transgenic mouse line. The raw data were motion corrected,d and individual cells were identified using non-negative matrix factorization. The dataset contains the spatial footprint of the cells and each time series of the measured Df/f fluorescence traces and the deconvolved activity stored in .mat files. All aanalysesperformed on the data can be reproduced using the MATLAB code in the GitHub repository: https://github.com/IEECR/In-vivo-analysis-of-medial-perforant-path-evoked-excitation-and-inhibition-in-dentate-granule-cells
- Patch clamp data on individual granule cells have been recorded in anesthetized animals incurrent-clampedd mode. Traces were recorded while the perforant path input was simulated using the opto-genetical toll ChRh2 in somata of LayerII cells in the medial entorhinal cortex. The raw traces are stored in .abf files, andthe analyzed data is stored in .mat files. The data analysis can be reproduced using code from: https://github.com/IEECR/In-vivo-analysis-of-medial-perforant-path-evoked-excitation-and-inhibition-in-dentate-granule-cells
Datasets are open to reproduce the results of the original study, and users are welcome to perform other analyses. Especially the imaging data and the control data set without stimulation are good examples of granule cell activity in vivo.
Photon imaging data: Functional calcium imaging data recorded from dentate granule cells in vivo in head-fixed awake mice. Imaging was performed with a standard Nikon 2-photon microscope at 940 nm excitation wavelength. The files contain the red out traces from individual cells as well as spatial footprints, deconvolved activity, and severalanalysess.
Data were recorded from individual granule cells in anesthetized mice. Cells were patched blindly and posthoc identified through filling of the cell body withbiocytinn. The files contain recordings at four different current injections and several trials for averaging.
Files and variables
File: CAIM-Baseline.mat
Description: 2P imaging data from baseline sessions with mice running ocue-enrichened belts
Variables
CAIM is a struct variable with one entry for each mouse in the dataset. Subfields are:
- behave: Behavioral readouts from the treadmill
- numrounds: Number of rounds the animal ran on the treadmil
- totdist: Total Distance the animal ran on the treadmil
- meanspeed: The average speed the animal had while running
- runtime: Accumulated time (s) the animal spend running
- pupil: Traces of the pupil diameter
- pupilsize: Stats (Mean, var, std-err) of the pupil while ruynning, standing and in total
- running: Boolean indicating times when the animal was running
- speed: Vector with running speed (cm/s)
- tsscn: Timestamps from the imaging scanner
- speedbin: Binned speed per bin on the running belt
- waitbin: Time spend resting on the running belt
- Y: raw fluorescence traces
- YC: Denoised flourescent traces
- Df: baseline fluorescence
- A: Spatial footprint
- Sraw: deconvolved activity traces
- S: Binary with Calcium event onsets
- Cn: Mean projection of FOV
- cclust: Parameters of each cell
- plcfield: Placefield analysis on linear track (Mean activity per round and bin)
- network: Analysis of synchronous activity
- Thresh: Threshold for a significant syncronous event
- pfit: P-values for different thresholds
- netev: binary vector with with frames of significant network events
- notps: indices of significant network events
- netprob: Probaility for each cell to take part in network events
- netfreq: stats for net work events during running, rest, and total
- netraster: Raster plot matrix containing population vectors from all network events
- netdist: pairwise Cos-distance between network events
- nethist: Histogram of network events sizes
- netshufflehist: Shuffled histograms
- celldist: Pariwise cos distance of cells considering only network-event related acitivty
- netnum: Number of cells per network event
- netresp: responses per network events
- cellsum: Number of synchronously active cells in each time bin
- replay: IDs or activated place cells during network events
- coact: Pairwise number of coactivations during network events
- intEvint: Inter event intervall betwenn network events
- speedcorr: Analysis of speed correlation
- cellID: Boolean whether cells were speed modulated
- bin: Speed bins
- trace: mean activity per speed bin per cell
- onsets: mean number of significant Ca event onsets per bin per cell
- error: Std error of acitivy per bin per cell
- fireprop: Activity properties of individual cells
- fire: Stats (Mean, std, std-error) of Ca events during run, rest, and total per cell
- firetot: Sum of events during run, rest and total per cell
- amplitude: Stats of events amplitudes (Mean, std, std-error) of Ca events during run, rest and total, per cell
- FOV: Stack of the field of view (x, y, cahnnel)
- bulk: Bulk fluorescencein different regions of the FOV
- crop{area}: Coordiantes for cropping in the FOV to get mean flouresnce
- thresh{area}: Threshold for signal to be considered
- trace{area}: Mean floujresnce trace over time for each channel
- template{area}: Boolean mask applied to the FOV for bulk read out
- runonset: Analysis of running behavior
- stimon: Times when mouse started running
- timepnt: indices when mouse started running
- pretime: inter running time
- stimplc: Place on treadmil where mouse started running
- cellID: IDs of significantly responding cells
- resp: binary traces around each running onset per cell
- respCa: Flouresence traces around running onset per cell
File: CAIM-AP.mat
Description: 2P imaging data from air puff sessions with mice running on cue-enriched belts
Variables
CAIM is a struct variable with one entry for each mouse in the dataset. Subfields are:
- behave: Behavioral readouts from the treadmill
- numrounds: Number of rounds the animal ran on the treadmil
- totdist: Total Distance the animal ran on the treadmil
- meanspeed: The average speed the animal had while running
- runtime: Accumulated time (s) the animal spend running
- pupil: Traces of the pupil diameter
- pupilsize: Stats (Mean, var, std-err) of the pupil while ruynning, standing and in total
- running: Boolean indicating times when the animal was running
- speed: Vector with running speed (cm/s)
- tsscn: Timestamps from the imaging scanner
- speedbin: Binned speed per bin on the running belt
- waitbin: Time spend resting on the running belt
- Y: raw fluorescence traces
- YC: Denoised flourescent traces
- Df: baseline fluorescence
- A: Spatial footprint
- Sraw: deconvolved activity traces
- S: Binary with Calcium event onsets
- Cn: Mean projection of FOV
- cclust: Parameters of each cell
- plcfield: Placefield analysis on linear track (Mean activity per round and bin)
- network: Analysis of synchronous activity
- Thresh: Threshold for a significant syncronous event
- pfit: P-values for different thresholds
- netev: binary vector with with frames of significant network events
- notps: indices of significant network events
- netprob: Probaility for each cell to take part in network events
- netfreq: stats for net work events during running, rest, and total
- netraster: Raster plot matrix containing population vectors from all network events
- netdist: pairwise Cos-distance between network events
- nethist: Histogram of network events sizes
- netshufflehist: Shuffled histograms
- celldist: Pariwise cos distance of cells considering only network-event related acitivty
- netnum: Number of cells per network event
- netresp: responses per network events
- cellsum: Number of synchronously active cells in each time bin
- replay: IDs or activated place cells during network events
- coact: Pairwise number of coactivations during network events
- intEvint: Inter event intervall betwenn network events
- speedcorr: Analysis of speed correlation
- cellID: Boolean whether cells were speed modulated
- bin: Speed bins
- trace: mean activity per speed bin per cell
- onsets: mean number of significant Ca event onsets per bin per cell
- error: Std error of acitivy per bin per cell
- fireprop: Activity properties of individual cells
- fire: Stats (Mean, std, std-error) of Ca events during run, rest, and total per cell
- firetot: Sum of events during run, rest and total per cell
- amplitude: Stats of events amplitudes (Mean, std, std-error) of Ca events during run, rest and total, per cell
- FOV: Stack of the field of view (x, y, cahnnel)
- bulk: Bulk fluorescencein different regions of the FOV
- crop{area}: Coordiantes for cropping in the FOV to get mean flouresnce
- thresh{area}: Threshold for signal to be considered
- trace{area}: Mean floujresnce trace over time for each channel
- template{area}: Boolean mask applied to the FOV for bulk read out
- airpuff: analysis of airpuff stimulation
- stimon: Times when stimulation was applied
- timepnt: indices when stimulation was applied
- pretime: inter stimulus time
- stimplc: Place on treadmil where stimulus was applied
- cellID: IDs of significantly responding cells
- resp: binary traces around each stimulus per cell
- respCa: Flouresence traces around stimuli per cell
- runonset: Analysis of running behavior
- stimon: Times when mouse started running
- timepnt: indices when mouse started running
- pretime: inter running time
- stimplc: Place on treadmil where mouse started running
- cellID: IDs of significantly responding cells
- resp: binary traces around each running onset per cell
- respCa: Flouresence traces around running onset per cell
File: M103.071216.1325pro.mat
Description: Example data set from a Thy1 mouse with a cranial window. This mouse is used for an example FOV and data inFiguree 1.
Variables
- caim: struct variable contained the raw fluorescence data (naming as for the pooled CAIM s.a.) and meta-analysis.
- belt: struct variable with the raw data from the running belt recorded at 100Hz. Variable names are self-explanatory.
- scn: Behavioral data from the belt variable, down-sampled and time-matched to the scanner recording frequency.
File: M234.071117.1642pro.mat
Description: Example data from a Thy1 mouse with injected jRGECO1a in MEC. This mouse is used for an example FOV and data in Figure 3.
Variables
- caim: struct variable contained the raw fluorescence data (naming as for the pooled CAIM s.a.) and meta-analysis.
- belt: struct variable with the raw data from the running belt recorded at 100Hz. Variable names are self-explanatory.
- scn: Behavioral data from the belt variable, down-sampled and time-matched to the scanner recording frequency.
File: PatchData.zip
Description:
- *.abf files: Raw patch data for every recording of individual cells from all the mice in the data set. The file can be opened with axoclamp software or by importing tools into other programs.
- *.mat files: Analyzed data from individual recording protocols of all cells in the data set. The data can be imported into MATLAB. Each file contains:
- vm: Measured voltages
- vi: inhibitory reversal potential
- ve: excitatory reversal potential
- time: time stamps
- stim: stimulation times
- sat: Saturation values for capacity fit
- rec: Reconstructed vm after model fit
- Ra: Access resistance
- prot: Number of protocol
- ongi: Onset of inhibitory conductances
- onge: Onset of excitatory conductances
- maxgi: maximum value of inhibitory conductance
- maxge: maximum value of excitatory conductance
- ljp: liquid junction potential
- gistd: standard deviation of inhibitory conductance at each time point
- gi: inhibitory conductance at each time point
- gestd: standard deviation of excitatory conductance at each time point
- ge: excitatory conductance at each time point
- expr: Histology data with expression images
- C: Fitted capacity of cells
- bsln: Baseline of each trace for every time point
- Mice.xls: Excel file containing info about every patch animal in the data set. the table contains the following columns:
- Mouse ID
- Strain
- Sex
- Birthdate
- Injection Date
- Virus used
- Injection coordinates
- Virus amount
- Remarks
- Date of Experiment
- Number of trials
- measured cells
- stimulation success
- remarks
- Laser power adjustment
- Biocytin expression
- mCherry expression
- Dapi expression
- slice containing the patched cell
- cells.xls: Excel file containing info about every patched cell in the data set with the following columns:
- Mouse ID
- Cell ID
- Recording Run
- z-depth in brain from surface
- Number of averaged cells
- Excitatory reversal potential Ve
- Inhibitory reversal potential Vi
- Resting potential Vr
- Liquid junction potential ljp
- Injected currents
- Used stimulation laser power
- Access resistance
- Pipette capacity
Code/software
All analysis code is available in git hub: https://github.com/IEECR/In-vivo-analysis-of-medial-perforant-path-evoked-excitation-and-inhibition-in-dentate-granule-cells
