{"id":23085795,"url":"https://github.com/neurodatawithoutborders/mat2nwb","last_synced_at":"2025-08-16T04:31:42.996Z","repository":{"id":35584120,"uuid":"39856725","full_name":"NeurodataWithoutBorders/mat2nwb","owner":"NeurodataWithoutBorders","description":"Conversion of Svoboda lab MATLAB files to NWB format.","archived":false,"fork":false,"pushed_at":"2017-05-12T13:14:43.000Z","size":105,"stargazers_count":5,"open_issues_count":0,"forks_count":6,"subscribers_count":26,"default_branch":"master","last_synced_at":"2023-10-26T00:19:32.091Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/NeurodataWithoutBorders.png","metadata":{"files":{"readme":"README","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2015-07-28T20:41:42.000Z","updated_at":"2022-06-14T03:19:04.000Z","dependencies_parsed_at":"2022-08-29T18:02:00.754Z","dependency_job_id":null,"html_url":"https://github.com/NeurodataWithoutBorders/mat2nwb","commit_stats":null,"previous_names":[],"tags_count":0,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NeurodataWithoutBorders%2Fmat2nwb","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NeurodataWithoutBorders%2Fmat2nwb/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NeurodataWithoutBorders%2Fmat2nwb/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NeurodataWithoutBorders%2Fmat2nwb/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/NeurodataWithoutBorders","download_url":"https://codeload.github.com/NeurodataWithoutBorders/mat2nwb/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":230005219,"owners_count":18158367,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-12-16T18:10:58.129Z","updated_at":"2024-12-16T18:10:58.834Z","avatar_url":"https://github.com/NeurodataWithoutBorders.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"This folder contains Python scripts: \n- mat2h5.py, make_nwb.py and mat2nwb.py, that allow conversion of data files \n  from MAT to NWB format (MAT =\u003e NWB), together with \n- several utility scripts for exploring the data in both \n  HDF5 and NWB files, and \n- a library file h5lib.py which defines the functions shared by all other scripts. \n\nFor a single input file, the MAT =\u003e NWB conversion can be performed in 2 steps:\n- MAT =\u003e HDF5 conversion, performed by the script mat2h5.py the resulting\n              HDF5 file preserves the structure of the original MAT file \n              as closely as possible; this step is not data-specific, i.e. \n              applicable to any MAT file, possibly comprising nested data \n              structures with arbitrary number of nesting levels; and\n- HDF5 =\u003e NWB conversion, performed by script make_nwb.py, which employs\n              NWB API (see the upper level folder \"api-python\");\n              this step is very data-specific; the current version of script\n              make_nwb.py supports conversion of data generated by \n              Dr. Karel Svoboda lab at Janelia Farm research facility of HHMI.\n\nThe script mat2nwb.py combines the two conversion steps in a pipeline that allows \nparallel conversion of large amounts of data using SGI compute cluster.\n\nNOTE: script mat2h5.py makes use of the loadmat function of scipy package.\n      We observed an issue (truncation of strings) when using this function \n      with Python 2.x on Scientific Linux platform ( see\n      https://github.com/scipy/scipy/issues/5984 ).\n      Because of this issue, the 1st of the two steps of conversion is\n      recommended to be performed using Python 3.x. \n      The second step works fine with Python 2.x.\n\nIn order to see usage of any script, type its name.\n\nTo see available options for scripts mat2h5.py, make_nwb.py and mat2nwb.py, \ntype the name of the script followed by flag \"-h\".\n\n\nExample of usage of the script mat2h5.py:\n\n    python3 mat2h5.py \u003cdata\u003e.mat               #   file \u003cdata\u003e.h5     will be produced\n    python3 mat2h5.py \u003cmetadata\u003e.mat           #   file \u003cmetadata\u003e.h5 will be produced\n\nExamples of usage of the script make_nwb.py:\n\n- if metadata is not included in the data file:\n    make_nwb.py  \u003cdata\u003e.h5 \u003cmetadata\u003e.h5      #   file \u003cdata\u003e.nwb will be produced\n- otherwise:\n    make_nwb.py  \u003cdata\u003e.h5                    #   file \u003cdata\u003e.nwb will be produced    \n\nExamples of usage of the script mat2h5.py:\n- on motor cortex data:\n    mat2nwb.py data_dir -M \n- on somatosensory cortex data:\n    mat2nwb.py data_dir -S\n\nwhere data_dir is a folder containing data and metadata files \nin the case of motor cortex data conversion and data files \nin the case of somatosensory cortex data conversion.\n\nTo make use of these scripts, the user must define environment variable\nNWB_DATA, which points to the full path to the root data directory.\nThis directory, in particular, will contain files data_collection.txt,\nexperiment_description.txt, and surgery.txt, which are used as additional metadata.\nAll the other data passed to the scripts may be specified as paths ralative to this \nroot directory.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fneurodatawithoutborders%2Fmat2nwb","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fneurodatawithoutborders%2Fmat2nwb","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fneurodatawithoutborders%2Fmat2nwb/lists"}