{"id":12618,"identifier":"CONCORDA/ITBQD4","persistentUrl":"https://hdl.handle.net/21.15109/CONCORDA/ITBQD4","protocol":"hdl","authority":"21.15109","publisher":"ARP","publicationDate":"2023-12-11","storageIdentifier":"s3-sztaki://21.15109/CONCORDA/ITBQD4","metadataLanguage":"en","datasetVersion":{"id":2239,"datasetId":12618,"datasetPersistentId":"hdl:21.15109/CONCORDA/ITBQD4","storageIdentifier":"s3-sztaki://21.15109/CONCORDA/ITBQD4","versionNumber":1,"versionMinorNumber":0,"versionState":"RELEASED","UNF":"UNF:6:gt0jsgTwuyd6CL27PiX3zg==","lastUpdateTime":"2023-12-11T19:59:22Z","releaseTime":"2023-12-11T19:59:22Z","createTime":"2023-10-03T12:29:59Z","publicationDate":"2023-12-11","citationDate":"2023-12-11","license":{"name":"CC0 1.0","uri":"http://creativecommons.org/publicdomain/zero/1.0","iconUri":"https://licensebuttons.net/p/zero/1.0/88x31.png"},"termsOfAccess":"Restricted files will be made available by requesting access.","contactForAccess":"To request access to the restricted files, please contact Richard Fiath (fiath.richard@ttk.hu).","fileAccessRequest":true,"metadataBlocks":{"citation":{"displayName":"Citation Metadata","name":"citation","fields":[{"typeName":"title","multiple":false,"typeClass":"primitive","value":"In vivo two-photon calcium imaging dataset obtained from the primary visual cortex of GCaMP6 mice during electrical microstimulation"},{"typeName":"title_hu","multiple":false,"typeClass":"primitive","value":"GCaMP6 génmódosított egerek elsődleges látókérgéből elektromos mikrostimuláció során kétfoton kalcium képalkotással készített in vivo adatcsomag"},{"typeName":"author","multiple":true,"typeClass":"compound","value":[{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Fiáth, Richárd"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"HUN-REN Természettudományi Kutatóközpont"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"},"authorIdentifier":{"typeName":"authorIdentifier","multiple":false,"typeClass":"primitive","value":"0000-0001-8732-2691"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Rácz, Melinda"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"HUN-REN Természettudományi Kutatóközpont"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"},"authorIdentifier":{"typeName":"authorIdentifier","multiple":false,"typeClass":"primitive","value":"0000-0002-6166-7699"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Horváth, Csaba"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"HUN-REN Természettudományi Kutatóközpont"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"},"authorIdentifier":{"typeName":"authorIdentifier","multiple":false,"typeClass":"primitive","value":"0000-0001-8176-8975"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Ulbert, István"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"HUN-REN Természettudományi Kutatóközpont"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"},"authorIdentifier":{"typeName":"authorIdentifier","multiple":false,"typeClass":"primitive","value":"0000-0001-9941-9159"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Wittner, Lucia"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"HUN-REN Természettudományi Kutatóközpont"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"},"authorIdentifier":{"typeName":"authorIdentifier","multiple":false,"typeClass":"primitive","value":"0000-0001-6800-0953"}}]},{"typeName":"datasetContact","multiple":true,"typeClass":"compound","value":[{"datasetContactName":{"typeName":"datasetContactName","multiple":false,"typeClass":"primitive","value":"Fiáth, Richárd"},"datasetContactAffiliation":{"typeName":"datasetContactAffiliation","multiple":false,"typeClass":"primitive","value":"ELKH Természettudományi Kutatóközpont"},"datasetContactEmail":{"typeName":"datasetContactEmail","multiple":false,"typeClass":"primitive","value":"fiath.richard@ttk.hu"}}]},{"typeName":"dsDescription","multiple":true,"typeClass":"compound","value":[{"dsDescriptionValue":{"typeName":"dsDescriptionValue","multiple":false,"typeClass":"primitive","value":"Here, 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)."}}]},{"typeName":"subject","multiple":true,"typeClass":"controlledVocabulary","value":["Medicine, Health and Life Sciences"]},{"typeName":"keyword","multiple":true,"typeClass":"compound","value":[{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"calcium imaging"}},{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"electrical microstimulation"}},{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"two-photon microscopy"}},{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"visual cortex"}},{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"GCaMP6 mice"}}]},{"typeName":"notesText","multiple":false,"typeClass":"primitive","value":"<h3>Dataset structure</h3>\n\n<p>Each calcium imaging data and corresponding metadata were packaged in the\n<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). </p>\n\n<p>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).</p>\n<br>\n\n<h3>NWB file structure</h3>\n<p>Each NWB file contains several main groups (which are similar to directories). The <i>acquisition</i> group contains the raw calcium imaging data (TwoPhotonSeries’) in a compressed form. The <i>general</i> 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 <i>stimulus</i> field of the <i>general</i> group.</p>\n<br>\n\n<h3>Interacting with NWB files</h3>\n<p>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):</p>\n<br>\n https://flatironinstitute.github.io/neurosift/?p=/nwb&url=FILE_URL<br>\n<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> \n<br>\n<br>\nUsers 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>. \nHere we provide an example on how users can import data from NWB files using the MATLAB-based MatNWB API.</p>\n<br>\nLoading a single frame of raw calcium data:\n<br>\n<br>\n<code>\n1.\tnwb = nwbRead('Mouse4_V1_stimulation_1.nwb');\n</code>\n<br>\n<code>\n2.\tframe = nwb.acquisition.get('TwoPhotonSeries').data.load([1,1,1],[512,512,1]);\n</code>\n<br>\n<br>\nIt is important to note that TwoPhotonSeries data types in NWB files are stored with frames (time) in the first dimension and frame size \n(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).\n<br><br>\n<p>We also provide a Matlab script (\"NWB_tutorial_script.m\") which can be used to load and visualize files in the dataset using MatNWB.</p>\n<br>"},{"typeName":"language","multiple":true,"typeClass":"controlledVocabulary","value":["English"]},{"typeName":"contributor","multiple":true,"typeClass":"compound","value":[{"contributorType":{"typeName":"contributorType","multiple":false,"typeClass":"controlledVocabulary","value":"Data Collector"},"contributorName":{"typeName":"contributorName","multiple":false,"typeClass":"primitive","value":"Horváth, Csaba; Rácz, Melinda; Fiáth, Richárd"}},{"contributorType":{"typeName":"contributorType","multiple":false,"typeClass":"controlledVocabulary","value":"Project Leader"},"contributorName":{"typeName":"contributorName","multiple":false,"typeClass":"primitive","value":"Wittner, Lucia; Ulbert, István; Fiáth, Richárd"}},{"contributorType":{"typeName":"contributorType","multiple":false,"typeClass":"controlledVocabulary","value":"Researcher"},"contributorName":{"typeName":"contributorName","multiple":false,"typeClass":"primitive","value":"Horváth, Csaba; Rácz, Melinda; Fiáth, Richárd; Wittner, Lucia; Ulbert, István"}},{"contributorType":{"typeName":"contributorType","multiple":false,"typeClass":"controlledVocabulary","value":"Work Package Leader"},"contributorName":{"typeName":"contributorName","multiple":false,"typeClass":"primitive","value":"Integrative Neurosciene Research Group"}},{"contributorType":{"typeName":"contributorType","multiple":false,"typeClass":"controlledVocabulary","value":"Research Group"},"contributorName":{"typeName":"contributorName","multiple":false,"typeClass":"primitive","value":"Integrative Neurosciene Research Group"}}]},{"typeName":"grantNumber","multiple":true,"typeClass":"compound","value":[{"grantNumberAgency":{"typeName":"grantNumberAgency","multiple":false,"typeClass":"primitive","value":"Horizon Europe EIC Pathfinder Challenges"},"grantNumberValue":{"typeName":"grantNumberValue","multiple":false,"typeClass":"primitive","value":"Grant agreement ID: 101071015 (HYPERSTIM)"}}]},{"typeName":"depositor","multiple":false,"typeClass":"primitive","value":"Fiáth, Richárd"},{"typeName":"dateOfDeposit","multiple":false,"typeClass":"primitive","value":"2023-10-03"},{"typeName":"kindOfData","multiple":true,"typeClass":"primitive","value":["experimental data (calcium imaging)"]},{"typeName":"software","multiple":true,"typeClass":"compound","value":[{"softwareVersion":{"typeName":"softwareVersion","multiple":false,"typeClass":"primitive","value":"0.4.4"}},{"softwareVersion":{"typeName":"softwareVersion","multiple":false,"typeClass":"primitive","value":"4.0.0.10943"}},{"softwareVersion":{"typeName":"softwareVersion","multiple":false,"typeClass":"primitive","value":"2019b"}}]},{"typeName":"relatedMaterial","multiple":true,"typeClass":"primitive","value":["NWB files were created using NeuroConv:\nhttps://neuroconv.readthedocs.io/en/main/"]},{"typeName":"otherReferences","multiple":true,"typeClass":"primitive","value":["https://hyperstim.eu/"]}]}},"files":[{"label":"Mouse1_V1_spontaneous_activity.avi","restricted":false,"directoryLabel":"GCaMP6s_spontaneous_activity","version":1,"datasetVersionId":2239,"dataFile":{"id":12700,"persistentId":"hdl:21.15109/CONCORDA/ITBQD4/59GZ3Y","pidURL":"https://hdl.handle.net/21.15109/CONCORDA/ITBQD4/59GZ3Y","filename":"Mouse1_V1_spontaneous_activity.avi","contentType":"video/avi","friendlyType":"AVI 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