{"$id":"https://schemas.pennsieve.io/formats/v1.json","formats":[{"description":"Portable Document Format.","edam":"format_3508","extensions":[".pdf"],"fileTypes":["PDF"],"id":"pdf","mediaTypes":["application/pdf"],"name":"PDF"},{"description":"Multiscale Electrophysiology Format.","extensions":[".mef"],"fileTypes":["MEF"],"id":"mef","mediaTypes":["application/vnd.pennsieve.mef"],"name":"MEF Timeseries"},{"description":"European Data Format biosignal timeseries.","extensions":[".edf"],"fileTypes":["EDF"],"id":"edf","mediaTypes":["application/vnd.pennsieve.edf"],"name":"EDF Timeseries"},{"description":"BioSemi Data Format biosignal timeseries.","extensions":[".bdf"],"fileTypes":["BDF"],"id":"bdf","mediaTypes":["application/vnd.pennsieve.bdf"],"name":"BDF Timeseries"},{"description":"National Instruments Technical Data Management Streaming.","extensions":[".tdm",".tdms"],"fileTypes":["TDMS"],"id":"tdms","mediaTypes":["application/vnd.pennsieve.tdms"],"name":"TDMS"},{"description":"Open Ephys acquisition recordings.","extensions":[".continuous",".spikes",".events",".openephys"],"fileTypes":["OpenEphys"],"id":"open-ephys","mediaTypes":["application/vnd.pennsieve.open-ephys"],"name":"Open Ephys"},{"description":"Persyst EEG recordings.","extensions":[".lay",".dat"],"fileTypes":["Persyst"],"id":"persyst","mediaTypes":["application/vnd.pennsieve.persyst"],"name":"Persyst"},{"description":"Digital Imaging and Communications in Medicine.","edam":"format_3548","extensions":[".dcm",".dicom"],"fileTypes":["DICOM"],"id":"dicom","mediaTypes":["application/dicom"],"name":"DICOM"},{"description":"Neuroimaging Informatics Technology Initiative volume.","edam":"format_3549","extensions":[".nii",".nii.gz",".nifti"],"fileTypes":["NIFTI"],"id":"nifti","mediaTypes":["application/x-nifti","application/x-nifti-gz"],"name":"NIfTI"},{"description":"Portable Network Graphics raster image.","edam":"format_3603","extensions":[".png"],"fileTypes":["PNG"],"id":"png","mediaTypes":["image/png"],"name":"PNG Image"},{"description":"BCI2000 brain-computer interface data.","fileTypes":["BCI2000"],"id":"bci2000","mediaTypes":["application/vnd.pennsieve.bci2000"],"name":"BCI2000"},{"description":"BNI1 timeseries data.","fileTypes":["BNI1"],"id":"bni1","mediaTypes":["application/vnd.pennsieve.bni1"],"name":"BNI1"},{"description":"WaveForm DataBase physiological signals.","fileTypes":["WFDB"],"id":"wfdb","mediaTypes":["application/vnd.pennsieve.wfdb"],"name":"WFDB"},{"description":"Carl Zeiss Image microscopy format.","extensions":[".czi"],"fileTypes":["CZI"],"id":"czi","mediaTypes":["application/vnd.pennsieve.czi"],"name":"CZI (Zeiss)"},{"description":"Aperio whole-slide imaging format.","extensions":[".svs"],"fileTypes":["Aperio"],"id":"aperio","mediaTypes":["application/vnd.pennsieve.aperio"],"name":"Aperio SVS"},{"description":"Pennsieve static viewer payload.","fileTypes":["StaticViewerData"],"id":"static-viewer-data","mediaTypes":["application/vnd.pennsieve.static-viewer-data"],"name":"Static Viewer Data"},{"description":"Pennsieve directory viewer payload.","fileTypes":["DirectoryViewerData"],"id":"directory-viewer-data","mediaTypes":["application/vnd.pennsieve.directory-viewer-data"],"name":"Directory Viewer Data"},{"description":"JavaScript Object Notation document.","edam":"format_3464","extensions":[".json"],"fileTypes":["Json"],"id":"json","mediaTypes":["application/json"],"name":"JSON"},{"description":"Comma-separated values tabular data.","edam":"format_3752","extensions":[".csv"],"fileTypes":["CSV"],"id":"csv","mediaTypes":["text/csv"],"name":"CSV"},{"description":"Tab-separated values tabular data.","edam":"format_3475","extensions":[".tsv"],"fileTypes":["TSV"],"id":"tsv","mediaTypes":["text/tab-separated-values"],"name":"TSV"},{"description":"Plain text document.","edam":"format_1964","extensions":[".txt",".text",".rtf"],"fileTypes":["Text"],"id":"text","mediaTypes":["text/plain"],"name":"Plain Text"},{"description":"Extensible Markup Language document.","edam":"format_2332","extensions":[".xml"],"fileTypes":["XML"],"id":"xml","mediaTypes":["application/xml"],"name":"XML"},{"description":"HyperText Markup Language document.","edam":"format_2331","extensions":[".html",".htm"],"fileTypes":["HTML"],"id":"html","mediaTypes":["text/html"],"name":"HTML"},{"description":"Microsoft Excel spreadsheet.","extensions":[".xls",".xlsx"],"fileTypes":["MSExcel"],"id":"ms-excel","mediaTypes":["application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","application/vnd.ms-excel"],"name":"Microsoft Excel"},{"description":"Microsoft Word document.","extensions":[".doc",".docx"],"fileTypes":["MSWord"],"id":"ms-word","mediaTypes":["application/vnd.openxmlformats-officedocument.wordprocessingml.document","application/msword"],"name":"Microsoft Word"},{"description":"MPEG-4 video container.","edam":"format_3997","extensions":[".mp4"],"fileTypes":["MP4"],"id":"mp4","mediaTypes":["video/mp4"],"name":"MP4 Video"},{"description":"WebM video container.","extensions":[".webm"],"fileTypes":["WEBM"],"id":"webm","mediaTypes":["video/webm"],"name":"WebM Video"},{"description":"Ogg video container.","extensions":[".ogg",".ogv"],"fileTypes":["OGG"],"id":"ogg","mediaTypes":["video/ogg"],"name":"Ogg Video"},{"description":"Apple QuickTime video container.","extensions":[".mov"],"fileTypes":["MOV"],"id":"mov","mediaTypes":["video/quicktime"],"name":"QuickTime Video"},{"description":"MATLAB MAT-file.","edam":"format_3626","extensions":[".mat",".mex"],"fileTypes":["MAT"],"id":"mat","mediaTypes":["application/x-matlab-data"],"name":"MATLAB Data"},{"description":"JPEG raster image.","edam":"format_3579","extensions":[".jpg",".jpeg"],"fileTypes":["JPEG"],"id":"jpeg","mediaTypes":["image/jpeg"],"name":"JPEG Image"},{"description":"JPEG 2000 raster image.","extensions":[".jp2",".jpx"],"fileTypes":["JPEG2000"],"id":"jpeg-2000","mediaTypes":["image/jp2"],"name":"JPEG 2000 Image"},{"description":"Zeiss LSM confocal microscopy.","extensions":[".lsm"],"fileTypes":["LSM"],"id":"lsm","mediaTypes":["application/vnd.pennsieve.lsm"],"name":"Zeiss LSM"},{"description":"Hamamatsu NDPI whole-slide image.","extensions":[".ndpi"],"fileTypes":["NDPI"],"id":"ndpi","mediaTypes":["application/vnd.pennsieve.ndpi"],"name":"Hamamatsu NDPI"},{"description":"Olympus OIB microscopy image.","extensions":[".oib"],"fileTypes":["OIB"],"id":"oib","mediaTypes":["application/vnd.pennsieve.oib"],"name":"Olympus OIB"},{"description":"Olympus OIF microscopy image.","extensions":[".oif"],"fileTypes":["OIF"],"id":"oif","mediaTypes":["application/vnd.pennsieve.oif"],"name":"Olympus OIF"},{"description":"Region-of-interest annotation.","extensions":[".roi"],"fileTypes":["ROI"],"id":"roi","mediaTypes":["application/vnd.pennsieve.roi"],"name":"ROI"},{"description":"Neuronal morphology SWC format.","extensions":[".swc"],"fileTypes":["SWC"],"id":"swc","mediaTypes":["application/vnd.pennsieve.swc"],"name":"SWC Morphology"},{"description":"Compressed reference-based genomic alignment.","edam":"format_3462","extensions":[".cram"],"fileTypes":["CRAM"],"id":"cram","mediaTypes":["application/x-cram"],"name":"CRAM Alignment"},{"description":"FreeSurfer MGH/MGZ volumetric image.","extensions":[".mgh",".mgz",".mgh.gz"],"fileTypes":["MGH"],"id":"mgh","mediaTypes":["application/vnd.pennsieve.mgh"],"name":"FreeSurfer MGH"},{"description":"Audio Video Interleave container.","edam":"format_3990","extensions":[".avi"],"fileTypes":["AVI"],"id":"avi","mediaTypes":["video/x-msvideo"],"name":"AVI Video"},{"description":"MATLAB source script.","edam":"format_4007","extensions":[".m"],"fileTypes":["MATLAB"],"id":"matlab","mediaTypes":["text/x-matlab"],"name":"MATLAB Script"},{"description":"Hierarchical Data Format version 5.","edam":"format_3590","extensions":[".hdf5",".h5"],"fileTypes":["HDF5"],"id":"hdf5","mediaTypes":["application/x-hdf5"],"name":"HDF5"},{"description":"Tagged Image File Format.","edam":"format_3591","extensions":[".tiff",".tif"],"fileTypes":["TIFF"],"id":"tiff","mediaTypes":["image/tiff"],"name":"TIFF Image"},{"description":"Open Microscopy Environment TIFF with OME-XML metadata.","edam":"format_3727","extensions":[".ome.tiff",".ome.tif",".ome.tf2",".ome.tf8",".ome.btf",".ome.xml"],"fileTypes":["OMETIFF"],"id":"ome-tiff","mediaTypes":["image/tiff; profile=ome-tiff"],"name":"OME-TIFF"},{"description":"Multiscale image in the OME-NGFF Zarr layout: a folder ending in .ome.zarr.","edam":"format_3915","extensions":[".ozx",".ome.zarr.zip"],"fileTypes":["OMEZarr"],"folderExtensions":[".ome.zarr"],"id":"ome-zarr","kind":"directory","mediaTypes":["application/vnd.pennsieve.ome-zarr"],"name":"OME-Zarr"},{"description":"Bruker multi-frame TIFF image.","extensions":[".brukertiff.gz"],"fileTypes":["BRUKERTIFF"],"id":"bruker-tiff","mediaTypes":["application/vnd.pennsieve.bruker-tiff"],"name":"Bruker TIFF"},{"description":"Graphics Interchange Format raster image.","edam":"format_3467","extensions":[".gif"],"fileTypes":["GIF"],"id":"gif","mediaTypes":["image/gif"],"name":"GIF Image"},{"description":"Mayo Clinic ANALYZE volumetric image.","extensions":[".img",".hdr"],"fileTypes":["ANALYZE"],"id":"analyze","mediaTypes":["application/vnd.pennsieve.analyze"],"name":"ANALYZE Image"},{"description":"NeuroExplorer timeseries data.","extensions":[".nex",".nex5"],"fileTypes":["NeuroExplorer"],"id":"neuro-explorer","mediaTypes":["application/vnd.pennsieve.neuro-explorer"],"name":"NeuroExplorer"},{"description":"Medical Imaging NetCDF volumetric image.","extensions":[".mnc"],"fileTypes":["MINC"],"id":"minc","mediaTypes":["application/vnd.pennsieve.minc"],"name":"MINC"},{"description":"Blackrock Microsystems electrophysiology data.","fileTypes":["Blackrock"],"id":"blackrock","mediaTypes":["application/vnd.pennsieve.blackrock"],"name":"Blackrock"},{"description":"Moberg CNS Monitor timeseries.","extensions":[".moberg.gz"],"fileTypes":["MobergSeries"],"id":"moberg-series","mediaTypes":["application/vnd.pennsieve.moberg-series"],"name":"Moberg Series"},{"description":"Generic opaque binary data.","fileTypes":["GenericData"],"id":"generic-data","mediaTypes":["application/octet-stream"],"name":"Generic Data"},{"description":"Blackfynn annotation bundle.","extensions":[".bfannot"],"fileTypes":["BFANNOT"],"id":"bfannot","mediaTypes":["application/vnd.pennsieve.bfannot"],"name":"Blackfynn Annotation"},{"description":"Blackfynn timeseries bundle.","extensions":[".bfts"],"fileTypes":["BFTS"],"id":"bfts","mediaTypes":["application/vnd.pennsieve.bfts"],"name":"Blackfynn Timeseries"},{"description":"Nicolet EEG recordings.","extensions":[".e"],"fileTypes":["Nicolet"],"id":"nicolet","mediaTypes":["application/vnd.pennsieve.nicolet"],"name":"Nicolet"},{"description":"Multiscale Electrophysiology Format version 3: a .mefd session folder of channel (.timd) and segment (.segd) folders.","extensions":[".mefd.gz"],"fileTypes":["MEF3"],"folderExtensions":[".mefd"],"id":"mef3","kind":"directory","mediaTypes":["application/vnd.pennsieve.mef3"],"name":"MEF3 Timeseries"},{"description":"Pennsieve's timeseries format: a Zarr v3 folder ending in .ts.zarr, with multi-resolution channels (TS-Zarr spec).","edam":"format_3915","extensions":[".ts.zarr.zip"],"fileTypes":["TSZarr"],"folderExtensions":[".ts.zarr"],"id":"ts-zarr","kind":"directory","mediaTypes":["application/vnd.pennsieve.ts-zarr"],"name":"TS-Zarr timeseries"},{"description":"Apache Arrow Feather columnar format.","extensions":[".feather"],"fileTypes":["Feather"],"id":"feather","mediaTypes":["application/vnd.apache.feather"],"name":"Apache Feather"},{"description":"Blackrock NEV/NSx neural event data.","extensions":[".nev",".ns1",".ns2",".ns3",".ns4",".ns5",".ns6",".nf3"],"fileTypes":["NEV"],"id":"nev","mediaTypes":["application/vnd.pennsieve.nev"],"name":"Blackrock NEV"},{"description":"CED Spike2 electrophysiology data.","extensions":[".smr"],"fileTypes":["Spike2"],"id":"spike2","mediaTypes":["application/vnd.pennsieve.spike2"],"name":"Spike2"},{"description":"Adobe Illustrator vector document.","extensions":[".ai",".svg"],"fileTypes":["AdobeIllustrator"],"id":"adobe-illustrator","mediaTypes":["application/postscript","image/svg+xml"],"name":"Adobe Illustrator"},{"description":"AFNI neuroimaging dataset.","extensions":[".afni"],"fileTypes":["AFNI"],"id":"afni","mediaTypes":["application/vnd.pennsieve.afni"],"name":"AFNI"},{"description":"AFNI BRIK/HEAD neuroimaging dataset.","extensions":[".brik",".head"],"fileTypes":["AFNIBRIK"],"id":"afni-brik","mediaTypes":["application/vnd.pennsieve.afni-brik"],"name":"AFNI BRIK/HEAD"},{"description":"ANSYS simulation project.","extensions":[".aedt"],"fileTypes":["Ansys"],"id":"ansys","mediaTypes":["application/vnd.pennsieve.ansys"],"name":"ANSYS"},{"description":"Binary Alignment Map for genomic reads.","edam":"format_2572","extensions":[".bam",".bcl",".bcl.gz"],"fileTypes":["BAM"],"id":"bam","mediaTypes":["application/x-bam"],"name":"BAM Alignment"},{"description":"BIODAC timeseries recordings.","extensions":[".tab"],"fileTypes":["BIODAC"],"id":"biodac","mediaTypes":["application/vnd.pennsieve.biodac"],"name":"BIODAC"},{"description":"BioPAC AcqKnowledge recordings.","extensions":[".acq"],"fileTypes":["BioPAC"],"id":"biopac","mediaTypes":["application/vnd.pennsieve.biopac"],"name":"BioPAC"},{"description":"COMSOL Multiphysics model file.","extensions":[".mph"],"fileTypes":["COMSOL"],"id":"comsol","mediaTypes":["application/vnd.pennsieve.comsol"],"name":"COMSOL Model"},{"description":"C++ source code.","extensions":[".cpp"],"fileTypes":["CPlusPlus"],"id":"cpp","mediaTypes":["text/x-c++src"],"name":"C++ Source"},{"description":"C# source code.","fileTypes":["CSharp"],"id":"csharp","mediaTypes":["text/x-csharp"],"name":"C# Source"},{"description":"Generic raw binary data file.","extensions":[".data",".bin",".raw"],"fileTypes":["Data"],"id":"data","mediaTypes":["application/octet-stream"],"name":"Raw Data"},{"description":"Docker container build recipe.","extensions":["Dockerfile"],"fileTypes":["Docker"],"id":"docker","mediaTypes":["text/x-dockerfile"],"name":"Dockerfile"},{"description":"Encapsulated PostScript image.","edam":"format_3466","extensions":[".eps",".ps"],"fileTypes":["EPS"],"id":"eps","mediaTypes":["application/postscript"],"name":"EPS"},{"description":"ISAC Flow Cytometry Standard file.","extensions":[".fcs"],"fileTypes":["FCS"],"id":"fcs","mediaTypes":["application/vnd.isac.fcs"],"name":"FCS Flow"},{"description":"FASTA biological sequence format.","edam":"format_1929","extensions":[".fasta"],"fileTypes":["FASTA"],"id":"fasta","mediaTypes":["application/x-fasta"],"name":"FASTA"},{"description":"FASTQ sequencing reads with quality scores.","edam":"format_1930","extensions":[".fastq"],"fileTypes":["FASTQ"],"id":"fastq","mediaTypes":["application/x-fastq"],"name":"FASTQ"},{"description":"FreeSurfer cortical surface data.","extensions":[".lh",".rh",".curv"],"fileTypes":["FreesurferSurface"],"id":"freesurfer-surface","mediaTypes":["application/vnd.pennsieve.freesurfer-surface"],"name":"FreeSurfer Surface"},{"description":"FreeSurfer FS-FAST fMRI data.","fileTypes":["FSFast"],"id":"fsfast","mediaTypes":["application/vnd.pennsieve.fsfast"],"name":"FS-FAST"},{"description":"Hierarchical Data Format (legacy).","edam":"format_3873","extensions":[".hdf",".hdf4",".h4",".he2",".he5"],"fileTypes":["HDF"],"id":"hdf","mediaTypes":["application/x-hdf"],"name":"HDF"},{"description":"Bitplane Imaris microscopy format.","extensions":[".ims"],"fileTypes":["Imaris"],"id":"imaris","mediaTypes":["application/vnd.pennsieve.imaris"],"name":"Imaris"},{"description":"Intan Technologies electrophysiology recordings.","extensions":[".rhd"],"fileTypes":["Intan"],"id":"intan","mediaTypes":["application/vnd.pennsieve.intan"],"name":"Intan"},{"description":"Current-voltage curve recordings.","extensions":[".ibw"],"fileTypes":["IVCurveData"],"id":"iv-curve-data","mediaTypes":["application/vnd.pennsieve.iv-curve-data"],"name":"IV Curve Data"},{"description":"Java source code.","fileTypes":["JAVA"],"id":"java","mediaTypes":["text/x-java-source"],"name":"Java Source"},{"description":"JavaScript source code.","extensions":[".js"],"fileTypes":["Javascript"],"id":"javascript","mediaTypes":["application/javascript"],"name":"JavaScript Source"},{"description":"Jupyter interactive notebook.","extensions":[".ipynb"],"fileTypes":["Jupyter"],"id":"jupyter","mediaTypes":["application/x-ipynb+json"],"name":"Jupyter Notebook"},{"description":"ADInstruments LabChart recordings.","extensions":[".adicht",".adidat"],"fileTypes":["LabChart"],"id":"labchart","mediaTypes":["application/vnd.pennsieve.labchart"],"name":"LabChart"},{"description":"Leica microscopy image format.","extensions":[".lif"],"fileTypes":["Leica"],"id":"leica","mediaTypes":["application/vnd.pennsieve.leica"],"name":"Leica"},{"description":"MATLAB figure file.","extensions":[".fig"],"fileTypes":["MatlabFigure"],"id":"matlab-figure","mediaTypes":["application/vnd.pennsieve.matlab-figure"],"name":"MATLAB Figure"},{"description":"Markdown document.","extensions":[".md"],"fileTypes":["Markdown"],"id":"markdown","mediaTypes":["text/markdown"],"name":"Markdown"},{"description":"Minitab statistical project.","extensions":[".mpj",".mtw",".mgf"],"fileTypes":["Minitab"],"id":"minitab","mediaTypes":["application/vnd.pennsieve.minitab"],"name":"Minitab"},{"description":"Neuralynx electrophysiology data.","extensions":[".ncs"],"fileTypes":["Neuralynx"],"id":"neuralynx","mediaTypes":["application/vnd.pennsieve.neuralynx"],"name":"Neuralynx"},{"description":"NWB neurophysiology data (HDF5-based).","extensions":[".nwb"],"fileTypes":["NeuroDataWithoutBorders"],"id":"nwb","mediaTypes":["application/x-hdf5; profile=nwb"],"name":"NeuroData Without Borders"},{"description":"Neurodata Without Borders stored with the Zarr backend (hdmf-zarr) instead of HDF5: a folder ending in .nwb.zarr. Same NWB data model; readers need Zarr support (e.g. PyNWB's NWBZarrIO).","folderExtensions":[".nwb.zarr"],"id":"nwb-zarr","kind":"directory","mediaTypes":["application/vnd.pennsieve.nwb-zarr"],"name":"NWB (Zarr)"},{"description":"NEURON simulation model source.","extensions":[".hoc",".mod"],"fileTypes":["Neuron"],"id":"neuron","mediaTypes":["application/vnd.pennsieve.neuron"],"name":"NEURON Model"},{"description":"Nihon Kohden EEG recordings.","fileTypes":["NihonKoden"],"id":"nihon-koden","mediaTypes":["application/vnd.pennsieve.nihon-koden"],"name":"Nihon Kohden"},{"description":"Nikon ND2 microscopy image.","extensions":[".nd2"],"fileTypes":["Nikon"],"id":"nikon","mediaTypes":["application/vnd.pennsieve.nikon"],"name":"Nikon Microscope"},{"description":"HEKA PatchMaster electrophysiology data.","extensions":[".pgf",".pul"],"fileTypes":["PatchMaster"],"id":"patch-master","mediaTypes":["application/vnd.pennsieve.patch-master"],"name":"PatchMaster"},{"description":"Molecular Devices pCLAMP recordings.","extensions":[".abf"],"fileTypes":["PClamp"],"id":"pclamp","mediaTypes":["application/vnd.pennsieve.pclamp"],"name":"pCLAMP"},{"description":"Plexon electrophysiology data.","fileTypes":["Plexon"],"id":"plexon","mediaTypes":["application/vnd.pennsieve.plexon"],"name":"Plexon"},{"description":"Microsoft PowerPoint presentation.","extensions":[".ppt",".pptx"],"fileTypes":["PowerPoint"],"id":"power-point","mediaTypes":["application/vnd.openxmlformats-officedocument.presentationml.presentation","application/vnd.ms-powerpoint"],"name":"Microsoft PowerPoint"},{"description":"Python source code.","edam":"format_3996","extensions":[".py"],"fileTypes":["Python"],"id":"python","mediaTypes":["text/x-python"],"name":"Python Source"},{"description":"R source code.","edam":"format_3999","extensions":[".r"],"fileTypes":["R"],"id":"r","mediaTypes":["text/x-r"],"name":"R Source"},{"description":"R serialized data workspace.","extensions":[".rdata"],"fileTypes":["RData"],"id":"rdata","mediaTypes":["application/vnd.pennsieve.rdata"],"name":"R Data"},{"description":"Unix shell script.","extensions":[".sh",".tcsh",".bash",".zsh"],"fileTypes":["Shell"],"id":"shell","mediaTypes":["application/x-sh"],"name":"Shell Script"},{"description":"SolidWorks CAD assembly or drawing.","extensions":[".sldasm",".slddrw"],"fileTypes":["SolidWorks"],"id":"solid-works","mediaTypes":["application/vnd.pennsieve.solid-works"],"name":"SolidWorks"},{"description":"Variant Call Format genomic variants.","edam":"format_3016","extensions":[".vcf"],"fileTypes":["VariantData"],"id":"vcf","mediaTypes":["application/x-vcf"],"name":"VCF Variant Data"},{"description":"YAML Ain't Markup Language document.","edam":"format_3750","extensions":[".yaml",".yml"],"fileTypes":["YAML"],"id":"yaml","mediaTypes":["application/yaml"],"name":"YAML"},{"description":"Compressed archive (ZIP or tar.gz).","edam":"format_3987","extensions":[".zip",".tar",".tar.gz"],"fileTypes":["ZIP"],"id":"zip","mediaTypes":["application/zip"],"name":"Zip Archive"},{"description":"A Zarr store (v2 or v3): a folder of chunked, compressed n-dimensional arrays with JSON metadata. Use OME-Zarr, NWB (Zarr) or TS-Zarr when the store follows one of those.","folderExtensions":[".zarr"],"id":"zarr","kind":"directory","mediaTypes":["application/vnd.pennsieve.zarr"],"name":"Zarr"},{"description":"A chunked n-dimensional array store from the Java ecosystem (Fiji, BigDataViewer): a folder ending in .n5.","folderExtensions":[".n5"],"id":"n5","kind":"directory","mediaTypes":["application/vnd.pennsieve.n5"],"name":"N5"},{"description":"Multi-resolution volumes, meshes or skeletons for Neuroglancer (large EM and light-sheet data): a folder with an info file at its root.","id":"neuroglancer-precomputed","kind":"directory","mediaTypes":["application/vnd.pennsieve.neuroglancer-precomputed"],"name":"Neuroglancer precomputed"},{"description":"A Micro-Manager 2 acquisition: a dataset folder of TIFF files with an NDTiff.index.","id":"micromanager-ndtiff","kind":"directory","mediaTypes":["application/vnd.pennsieve.micromanager-ndtiff"],"name":"Micro-Manager NDTiff"},{"description":"Bruker preclinical MRI raw data: a study or scan folder with acqp and method files and reconstructions under pdata/.","id":"bruker-paravision","kind":"directory","mediaTypes":["application/vnd.pennsieve.bruker-paravision"],"name":"Bruker ParaVision"},{"description":"Tractography streamlines and their data: a folder of arrays with a header.json, also used zipped as a .trx file.","id":"trx","kind":"directory","mediaTypes":["application/vnd.pennsieve.trx"],"name":"TRX tractography"},{"description":"The current Open Ephys recording format: a recording folder with structure.oebin and continuous/ and events/ folders.","id":"open-ephys-binary","kind":"directory","mediaTypes":["application/vnd.pennsieve.open-ephys-binary"],"name":"Open Ephys binary"},{"description":"A clinical EEG or long-term monitoring study from Natus NeuroWorks (formerly Xltek): a study folder of .erd, .etc, .ent, .snc, .stc and .vtc files.","id":"natus-neuroworks","kind":"directory","mediaTypes":["application/vnd.pennsieve.natus-neuroworks"],"name":"Natus NeuroWorks (Xltek)"},{"description":"A Compumedics ProFusion EEG or sleep study: a study folder of the recording's files.","id":"compumedics-profusion","kind":"directory","mediaTypes":["application/vnd.pennsieve.compumedics-profusion"],"name":"Compumedics ProFusion"},{"description":"A Tucker-Davis Technologies recording block: a folder of .tev, .tsq, .tbk and related files, read together.","id":"tdt-block","kind":"directory","mediaTypes":["application/vnd.pennsieve.tdt-block"],"name":"Tucker-Davis (TDT) block"},{"description":"A SpikeGLX acquisition (Neuropixels): a run folder (*_g0) of .bin data files, each with its .meta file.","id":"spikeglx","kind":"directory","mediaTypes":["application/vnd.pennsieve.spikeglx"],"name":"SpikeGLX run"},{"description":"An Illumina sequencing run: a folder with RunInfo.xml and base calls (BCL) under Data/Intensities/BaseCalls/.","id":"illumina-run","kind":"directory","mediaTypes":["application/vnd.pennsieve.illumina-run"],"name":"Illumina run folder"},{"description":"Bruker mass spectrometry data (e.g. timsTOF): a folder ending in .d with an analysis.tdf. Agilent also uses .d folders; see Agilent .d.","id":"bruker-d","kind":"directory","mediaTypes":["application/vnd.pennsieve.bruker-d"],"name":"Bruker .d"},{"description":"Agilent mass spectrometry data: a folder ending in .d with an AcqData folder. Bruker also uses .d folders; see Bruker .d.","id":"agilent-d","kind":"directory","mediaTypes":["application/vnd.pennsieve.agilent-d"],"name":"Agilent .d"},{"description":"Waters mass spectrometry data: a folder ending in .raw (unlike Thermo .raw, which is a file).","id":"waters-raw","kind":"directory","mediaTypes":["application/vnd.pennsieve.waters-raw"],"name":"Waters .raw"},{"description":"10x Genomics counts (Cell Ranger, Space Ranger): a folder with matrix.mtx.gz, barcodes.tsv.gz and features.tsv.gz.","id":"tenx-feature-barcode-matrix","kind":"directory","mediaTypes":["application/vnd.pennsieve.tenx-feature-barcode-matrix"],"name":"10x feature-barcode matrix"},{"description":"Single-cell data as TileDB arrays (as used by CELLxGENE Census): a folder of arrays and groups.","id":"tiledb-soma","kind":"directory","mediaTypes":["application/vnd.pennsieve.tiledb-soma"],"name":"TileDB-SOMA"},{"description":"An imaging mass cytometry acquisition (Hyperion), with its panoramas and regions of interest.","extensions":[".mcd"],"id":"imc-mcd","mediaTypes":["application/vnd.pennsieve.imc-mcd"],"name":"Imaging mass cytometry (MCD)"},{"description":"An annotated data matrix for single-cell data (scanpy, AnnData), stored as HDF5.","extensions":[".h5ad"],"id":"anndata","mediaTypes":["application/x-hdf5; profile=anndata"],"name":"AnnData (h5ad)"},{"description":"The open mass spectrometry data format from HUPO-PSI (XML).","extensions":[".mzml",".mzML"],"id":"mzml","mediaTypes":["application/vnd.pennsieve.mzml"],"name":"mzML"},{"description":"Raw Oxford Nanopore signal data.","extensions":[".pod5"],"id":"pod5","mediaTypes":["application/vnd.pennsieve.pod5"],"name":"Oxford Nanopore POD5"},{"description":"A single R object saved with saveRDS: a Seurat, SingleCellExperiment or any other R object. Apps say which object they expect in their description.","extensions":[".rds"],"id":"rds","mediaTypes":["application/x-rds"],"name":"R object (RDS)"},{"description":"Columnar table file (Apache Parquet).","extensions":[".parquet"],"id":"parquet","mediaTypes":["application/vnd.apache.parquet"],"name":"Apache Parquet"},{"description":"A Seurat object stored as HDF5 (SeuratDisk).","extensions":[".h5seurat"],"id":"h5seurat","mediaTypes":["application/x-hdf5; profile=h5seurat"],"name":"h5Seurat"},{"description":"Single-cell expression matrix with row and column attributes, stored as HDF5.","extensions":[".loom"],"id":"loom","mediaTypes":["application/x-hdf5; profile=loom"],"name":"Loom"},{"description":"Multimodal single-cell data (muon, MuData), stored as HDF5.","extensions":[".h5mu"],"id":"mudata","mediaTypes":["application/x-hdf5; profile=mudata"],"name":"MuData (h5mu)"},{"description":"10x Genomics counts as one HDF5 file (filtered_feature_bc_matrix.h5); the same data as the 10x feature-barcode matrix folder.","id":"tenx-h5","mediaTypes":["application/x-hdf5; profile=tenx-h5"],"name":"10x feature-barcode matrix (HDF5)"},{"description":"Single-cell ATAC fragments (fragments.tsv.gz, usually with its .tbi index), as used by Signac, ArchR and Cell Ranger ATAC.","id":"atac-fragments","mediaTypes":["application/vnd.pennsieve.atac-fragments"],"name":"ATAC fragments"},{"description":"An on-disk counts matrix written by BPCells (used by Seurat v5 for large data): a folder of the matrix's binary files.","id":"bpcells-matrix","kind":"directory","mediaTypes":["application/vnd.pennsieve.bpcells-matrix"],"name":"BPCells matrix"},{"description":"An AnnData object stored as Zarr instead of HDF5: a folder (usually ending in .zarr).","id":"anndata-zarr","kind":"directory","mediaTypes":["application/vnd.pennsieve.anndata-zarr"],"name":"AnnData (Zarr)"},{"description":"Spatial omics data (SpatialData): a Zarr folder of images (OME-Zarr), labels, points, shapes and tables.","id":"spatialdata-zarr","kind":"directory","mediaTypes":["application/vnd.pennsieve.spatialdata-zarr"],"name":"SpatialData (Zarr)"},{"description":"10x Genomics Visium results: the outs folder with the counts matrix and spatial/ (images and spot positions).","id":"spaceranger-outs","kind":"directory","mediaTypes":["application/vnd.pennsieve.spaceranger-outs"],"name":"Space Ranger output (Visium)"},{"description":"10x Genomics Xenium results: a folder with experiment.xenium, transcripts, cells and morphology images.","id":"xenium-bundle","kind":"directory","mediaTypes":["application/vnd.pennsieve.xenium-bundle"],"name":"Xenium output bundle"},{"description":"Vizgen MERSCOPE results: a region folder with cell-by-gene counts, cell metadata, detected transcripts and images.","id":"merscope-output","kind":"directory","mediaTypes":["application/vnd.pennsieve.merscope-output"],"name":"MERSCOPE output"},{"description":"NanoString/Bruker CosMx SMI results: a folder of expression matrix, metadata, transcript and field-of-view files.","id":"cosmx-output","kind":"directory","mediaTypes":["application/vnd.pennsieve.cosmx-output"],"name":"CosMx output"},{"description":"A single-cell ATAC analysis project from ArchR: a folder with the saved project and its Arrow files.","id":"archr-project","kind":"directory","mediaTypes":["application/vnd.pennsieve.archr-project"],"name":"ArchR project"},{"description":"One table split into many Parquet files in a folder (often partitioned by column, e.g. year=2024/).","id":"parquet-dataset","kind":"directory","mediaTypes":["application/vnd.pennsieve.parquet-dataset"],"name":"Partitioned Parquet dataset"}],"schemaVersion":"1.2.0","structures":[{"description":"Brain Imaging Data Structure: a folder layout and naming scheme for neuroimaging and physiology studies (sub-*/ses-*/\u003cmodality\u003e/), with a dataset_description.json at the root. Covers MRI, EEG, iEEG, MEG, PET, microscopy and more; derivatives follow it too.","id":"bids","name":"BIDS","spec":"https://bids-specification.readthedocs.io/","uri":"https://bids.neuroimaging.io/","validator":"https://github.com/bids-standard/bids-validator"},{"description":"The SPARC program's dataset layout: primary/, derivative/, code/, docs/ and protocol/ folders, with dataset_description, subjects and samples sheets at the root.","id":"sparc-sds","name":"SPARC Dataset Structure (SDS)","spec":"https://github.com/SciCrunch/sparc-curation","uri":"https://github.com/SciCrunch/sparc-curation"},{"contentRoot":"files","description":"A dataset as Pennsieve publishes it: manifest.json (schema.org Dataset metadata listing every file), readme.md, changelog.md and banner.jpg at the root, and the data under files/. The data under files/ may follow another structure, such as BIDS.","id":"pennsieve-published-dataset","name":"Pennsieve Published Dataset (PPD)","spec":"https://schemas.pennsieve.io/structures/pennsieve-published-dataset/v5.0","uri":"https://schemas.pennsieve.io/structures/pennsieve-published-dataset","versions":["1","2","3.0","4.0","5.0"]},{"description":"A folder described by an ro-crate-metadata.json at its root: the files, their formats (encodingFormat) and which specifications the folder follows (conformsTo). Pennsieve views are RO-Crates.","id":"ro-crate","name":"RO-Crate","spec":"https://w3id.org/ro/crate","uri":"https://w3id.org/ro/crate"}]}