In vivo two-photon calcium imaging dataset obtained from the primary visual cortex of GCaMP6 mice during electrical microstimulationhdl:21.15109/CONCORDA/ITBQD4ARP2023-12-111Fiáth, Richárd; Rácz, Melinda; Horváth, Csaba; Ulbert, István; Wittner, Lucia, 2023, "In vivo two-photon calcium imaging dataset obtained from the primary visual cortex of GCaMP6 mice during electrical microstimulation", https://hdl.handle.net/21.15109/CONCORDA/ITBQD4, ARP, V1, UNF:6:gt0jsgTwuyd6CL27PiX3zg== [fileUNF]In vivo two-photon calcium imaging dataset obtained from the primary visual cortex of GCaMP6 mice during electrical microstimulationhdl:21.15109/CONCORDA/ITBQD4Fiáth, RichárdRácz, MelindaHorváth, CsabaUlbert, IstvánWittner, LuciaHorváth, Csaba; Rácz, Melinda; Fiáth, RichárdWittner, Lucia; Ulbert, István; Fiáth, RichárdHorváth, Csaba; Rácz, Melinda; Fiáth, Richárd; Wittner, Lucia; Ulbert, IstvánIntegrative Neurosciene Research GroupIntegrative Neurosciene Research GroupNeuroConvMEScMATLABGrant agreement ID: 101071015 (HYPERSTIM)ARPFiáth, RichárdFiáth, Richárd2023-10-03Medicine, Health and Life Sciencescalcium imagingelectrical microstimulationtwo-photon microscopyvisual cortexGCaMP6 miceHere, we deposited a calcium imaging dataset collected within the framework of the <a href="https://hyperstim.eu/">HYPERSTIM</a> Horizon Europe project. The in vivo dataset was obtained from the primary visual cortex of GCaMP6 transgenic mice during electrical microstimulation using a two-photon laser scanning microscope. A subset of the dataset contains spontaneous cortical activity without electrical stimulation (Mouse1 and Mouse2). Mice were anesthetized with ketamine/xylazine. A Femtonics Femto2D two-photon microscope setup was used for data acquisition. A 20x water immersion objective with the following parameters was used for calcium imaging. Field of view (FOV): 550 μm x 550 μm; Numerical aperture (NA): 1.0; Working distance: 2.0 mm. We performed raster scanning with a resonant scanner at ~31 Hz frame rate and with a frame size of 512 x 512 pixels. The wavelength used for calcium imaging was 900 nm. Further details can be found below (see Notes).experimental data (calcium imaging)<h3>Dataset structure</h3> Each calcium imaging data and corresponding metadata were packaged in the <a href="https://www.nwb.org/">Neurodata Without Borders: Neurophysiology version 2.0 (NWB:N 2.0) data format</a> using the <a href="https://github.com/catalystneuro/neuroconv">NeuroConv Python package</a>. A single NWB file was created from each data file. NWB files were placed in folders based on the calcium indicator used (GCaMP6s or GCaMP6f), and whether it was a spontaneous measurement or electrical stimulation was performed during calcium imaging. The filename of the NWB file (identifier; e.g., Mouse3_V1_stimulation_x) was constructed by concatenating the identifier of the animal, the targeted brain area (V1) and the type of the recording (stimulation/spontaneous). For each NWB file, we also included a video file in AVI format showing the calcium activity with the same frame rate as they were collected (with the exception of spontaneous data which is shown at a 3x speed). The CSV file named "Subject_characteristics" contains information about the animals used for calcium imaging such as the species, weight, sex, age or genotype. The "Recording_characteristics" CSV file lists several useful properties for each NWB file including the file size, the duration of the measurement, the targeted cortical area, the imaging depth or the stimulus parameters (e.g., current amplitude, stimulation frequency, pulse duration or number of stimulation trials). <h3>NWB file structure</h3> Each NWB file contains several main groups (which are similar to directories). The acquisition group contains the raw calcium imaging data (TwoPhotonSeries’) in a compressed form. The general group contains metadata about the experiments and consists of several subgroups, related to the two-photon microscope used (‘general/devices/Microscope’), calcium imaging parameters ('general/optophysiology) and subjects of the experiments (‘general/subject’). Former subgroups carry information about the two-photon microscope setup, the imaged brain area and the properties of calcium imaging, while the latter contains metadata about the animal (e.g., species, genotype, subject ID, or weight). The stimulus parameters are described in the stimulus field of the general group. <h3>Interacting with NWB files</h3> After downloading, the structure of NWB files can be explored using the <a href="https://www.hdfgroup.org/downloads/hdfview/">HDFView</a> software.<a href="https://github.com/flatironinstitute/neurosift">Neurosift </a>can be used to open NWB files in a browser and explore their contents using the download URL of the selected data file (e.g. https://science-data.hu/api/access/datafile/17276): https://flatironinstitute.github.io/neurosift/?p=/nwb&url=FILE_URL <a href="https://flatironinstitute.github.io/neurosift/?p=/nwb&url=https://science-data.hu/api/access/datafile/17276">https://flatironinstitute.github.io/neurosift/?p=/nwb&url=https://science-data.hu/api/access/datafile/17276</a> Users can import data from NWB files offline using the <a href="https://github.com/NeurodataWithoutBorders/pynwb/">PyNWB</a> and <a href="https://github.com/NeurodataWithoutBorders/matnwb/">MatNWB</a> APIs, or using <a href="https://github.com/SpikeInterface">SpikeInterface</a>. Here we provide an example on how users can import data from NWB files using the MATLAB-based MatNWB API. Loading a single frame of raw calcium data: <code> 1. nwb = nwbRead('Mouse4_V1_stimulation_1.nwb'); </code> <code> 2. frame = nwb.acquisition.get('TwoPhotonSeries').data.load([1,1,1],[512,512,1]); </code> It is important to note that TwoPhotonSeries data types in NWB files are stored with frames (time) in the first dimension and frame size (512 x 512) in the second and third dimensions, but dimensions are reversed in MatNWB (i.e., the time/frame is stored in the third dimension). We also provide a Matlab script ("NWB_tutorial_script.m") which can be used to load and visualize files in the dataset using MatNWB. To request access to the restricted files, please contact Richard Fiath (fiath.richard@ttk.hu).Restricted files will be made available by requesting access.NWB files were created using NeuroConv: https://neuroconv.readthedocs.io/en/main/https://hyperstim.eu/Recording_characteristics.tab8316text/tab-separated-valuesUNF:6:qilGYeowgS9+2EXb/mzHlQ==Subject_characteristics.tab47text/tab-separated-valuesUNF:6:mEcw4wntwDcPZrRcXLNz8g==NWB file nameUNF:6:7a8y3GNWJGDO8TvbVBZ62w==NWB file size (MB)882.9122.56393126261560.0.44.1114.06265060240963113.383.0UNF:6:c5psYH9HMlEfBgEHNMyOxQ==Recording duration (sec)83.0360.037.5180722891566235.044.676168538304730.020.0.UNF:6:TrcUpUClOmvygjFukdrRtg==Number of frames11164.01158.7228915662651085.00.0.83.01386.657758550262614.0UNF:6:zy5YMzYIspimiV0aKzXn9Q==Imaging frame rate (Hz).30.975230.975230.97520.083.00.030.9752UNF:6:ytwURoNoXSsl2/boogmJ4A==Targeted brain areaUNF:6:+LMczmNGqXnNSCO8d5Mqew==Imaging depth (um from the surface of the cortex)0.0.83.036.54115420497544117.01204819277109188.0132.051.0UNF:6:t6AEkX2WcOv/oSGn9RmPFA==Start of the stimulation (frame ID)UNF:6:pnNHpcGE6/kzWPda+/vhkA==Number of stimulation pulsesUNF:6:toI98PrWRUjiy7kpfDX+4g==Current amplitude (uA)UNF:6:WlKSN5eZh44xNZCAc0QZXw==Pulse duration (us. one phase)UNF:6:+wBOscaqQRNkHqkRWKDQBg==Interphase interval (us)UNF:6:z+VQXaC6zWh78DjKhph+HA==Frequency of stimulation (Hz)UNF:6:QD+k26k8/e5Hucr7RD5OPg==Number of trials (stimulus repeats)UNF:6:3849ZWcIf4mj7lS+y1vO3g==Trial delay (ms)UNF:6:SRbdj7SEaNtIqxwAng96/A==ID of microelectrode used for stimulationUNF:6:VkC0QD8B9IHGdkLv5nguNA==Animal IDUNF:6:TTwZcrHSrGfO3zNov7EHVw==Weight (g).7.0887234393789134.020.00.035.025.2523.0UNF:6:QlM+0PGtj3dAf1iUdL+dBQ==SexUNF:6:PAOpbagdANqanD0a4HMetA==SpeciesUNF:6:6ekd4xhZLHet0DkryluKeg==StrainUNF:6:Z7GIN0B5oY4591VHa8j10Q==GenotypeUNF:6:kTQzferWMh+Lp2p43slEcQ==Age 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