From 304da82ccff8ddee17bfdaa7f2c9efaae19f5952 Mon Sep 17 00:00:00 2001 From: CodyCBakerPhD Date: Sat, 20 Aug 2022 21:29:34 +0000 Subject: [PATCH] removed unused files --- metadatafiles/nct_ophys_metafile_cnmfe.yaml | 57 ------ metadatafiles/nct_ophys_metafile_extract.yaml | 55 ------ metadatafiles/nct_ophys_metafile_nwb.yaml | 62 ------- metadatafiles/nct_ophys_metafile_sima.yaml | 58 ------ metadatafiles/nct_ophys_metafile_suite2p.yaml | 62 ------- metadatafiles/nwbwriter.schema.json | 172 ------------------ 6 files changed, 466 deletions(-) delete mode 100644 metadatafiles/nct_ophys_metafile_cnmfe.yaml delete mode 100644 metadatafiles/nct_ophys_metafile_extract.yaml delete mode 100644 metadatafiles/nct_ophys_metafile_nwb.yaml delete mode 100644 metadatafiles/nct_ophys_metafile_sima.yaml delete mode 100644 metadatafiles/nct_ophys_metafile_suite2p.yaml delete mode 100644 metadatafiles/nwbwriter.schema.json diff --git a/metadatafiles/nct_ophys_metafile_cnmfe.yaml b/metadatafiles/nct_ophys_metafile_cnmfe.yaml deleted file mode 100644 index eeec16b0..00000000 --- a/metadatafiles/nct_ophys_metafile_cnmfe.yaml +++ /dev/null @@ -1,57 +0,0 @@ ---- -NWBFile: - session_start_time: 2020-02-02 00:00:00 - keywords: [cnmfe] - experiment_description: brief experiment description - session_id: session id goes here - experimenter: [testname] - identifier: nwbfile id - institution: inistitution name - lab: lab name - session_description: ses desc - surgery: surgery description - pharmacology: pharma - protocol: protocol used - related_publications: [pub1, pub2] - notes: nwbfile notes - virus: virus info -Subject: - subject_id: subjectID - description: subject descriptoin - genotype: genotype - sex: F - species: species - weight: weight number - date_of_birth: 2010-02-02 00:00:00 -Ophys: - Device: - - name: ophys_Device1 - description: ophys_device1_description - - name: ophys_Device2 - description: ophys_device2_description - Fluorescence: - name: df_over_f_name - roi_response_series: - - name: RoiResponseSeries - description: description of roi resp series - ImageSegmentation: - name: ABCD - plane_segmentations: - - name: MyplaneSegmentation - description: Segmented ROIs - ImagingPlane: - - description: standard - excitation_lambda: 600.0 - imaging_rate: 1.0 - indicator: GCaMP - location: V1 - name: ImagingPlane - grid_spacing: [2,2] - grid_spacing_unit: microns - optical_channels: - - name: OpticalChannel - emission_lambda: 500.0 - description: description - TwoPhotonSeries: - - name: TwoPhotonSeries - description: description diff --git a/metadatafiles/nct_ophys_metafile_extract.yaml b/metadatafiles/nct_ophys_metafile_extract.yaml deleted file mode 100644 index 51868a61..00000000 --- a/metadatafiles/nct_ophys_metafile_extract.yaml +++ /dev/null @@ -1,55 +0,0 @@ ---- -NWBFile: - session_start_time: 2020-02-02 00:00:00 - keywords: [extractmethod] - experiment_description: brief experiment description - session_id: session id goes here - experimenter: [testname] - identifier: nwbfile id - institution: inistitution name - lab: lab name - session_description: ses desc - surgery: surgery description - pharmacology: pharma - protocol: protocol used - related_publications: [pub1, pub2] - notes: nwbfile notes - virus: virus info -Subject: - subject_id: subjectID - description: subject descriptoin - genotype: genotype - sex: F - species: species - weight: weight number - date_of_birth: 2010-02-02 00:00:00 -Ophys: - Device: - - name: ophys_Device1 - description: ophys_device1_description - Fluorescence: - name: Fluorescence - roi_response_series: - - name: RoiResponseSeries - description: description of roi resp series - ImageSegmentation: - name: ABCD - plane_segmentations: - - name: MyplaneSegmentation - description: Segmented ROIs - ImagingPlane: - - description: standard - excitation_lambda: 600.0 - imaging_rate: 1.0 - indicator: GCaMP - location: V1 - name: ImagingPlane - grid_spacing: [2,2] - grid_spacing_unit: microns - optical_channels: - - name: OpticalChannel - emission_lambda: 500.0 - description: description - TwoPhotonSeries: - - name: TwoPhotonSeries - description: description diff --git a/metadatafiles/nct_ophys_metafile_nwb.yaml b/metadatafiles/nct_ophys_metafile_nwb.yaml deleted file mode 100644 index aab232a6..00000000 --- a/metadatafiles/nct_ophys_metafile_nwb.yaml +++ /dev/null @@ -1,62 +0,0 @@ ---- -NWBFile: - session_start_time: 2020-02-02 00:00:00 - keywords: [keyword1, keyword2] - experiment_description: My two-photon microscope - session_id: session id goes here - experimenter: [testname] - identifier: nwbfile id - institution: inistitution name - lab: lab name - session_description: ses desc - surgery: surgery description - pharmacology: pharma - protocol: protocol used - related_publications: [pub1, pub2] - notes: nwbfile notes - virus: virus info -Subject: - subject_id: subjectID - description: subject descriptoin - genotype: genotype - sex: F - species: species - weight: weight number - date_of_birth: 2010-02-02 00:00:00 -Ophys: - Device: - - name: Microscope - description: ophys_device1_description - Fluorescence: - name: Fluorescence - roi_response_series: - - name: RoiResponseSeries - description: array of fluorescence traces - - name: Neuropil - description: array of neuropil fluorescence traces - - name: Deconvolved - description: array of deconvolved traces - ImageSegmentation: - name: ABCD - plane_segmentations: - - name: MyplaneSegmentation - description: Segmented ROIs - ImagingPlane: - - description: standard - excitation_lambda: 600.0 - imaging_rate: 1.0 - indicator: GCaMP - location: V1 - name: ImagingPlane - grid_spacing: [2,2] - grid_spacing_unit: microns - optical_channels: - - name: OpticalChannel1 - emission_lambda: 500.0 - description: description - - name: OpticalChannel2 - emission_lambda: 500.0 - description: description - TwoPhotonSeries: - - name: TwoPhotonSeries - description: description diff --git a/metadatafiles/nct_ophys_metafile_sima.yaml b/metadatafiles/nct_ophys_metafile_sima.yaml deleted file mode 100644 index 841ca444..00000000 --- a/metadatafiles/nct_ophys_metafile_sima.yaml +++ /dev/null @@ -1,58 +0,0 @@ ---- -NWBFile: - session_start_time: 2020-02-02 00:00:00 - keywords: [SIMA] - experiment_description: My two-photon microscope - session_id: session id goes here - experimenter: [testname] - identifier: nwbfile id - institution: inistitution name - lab: lab name - session_description: ses desc - surgery: surgery description - pharmacology: pharma - protocol: protocol used - related_publications: [pub1, pub2] - notes: nwbfile notes - virus: virus info -Subject: - subject_id: subjectID - description: subject descriptoin - genotype: genotype - sex: F - species: species - weight: weight number - date_of_birth: 2010-02-02 00:00:00 -Ophys: - Device: - - name: Microscope - description: ophys_device1_description - Fluorescence: - name: Fluorescence - roi_response_series: - - name: RoiResponseSeries - description: array of fluorescence traces - ImageSegmentation: - name: ABCD - plane_segmentations: - - name: MyplaneSegmentation - description: Segmented ROIs - ImagingPlane: - - description: standard - excitation_lambda: 600.0 - imaging_rate: 1.0 - indicator: GCaMP - location: V1 - name: ImagingPlane - grid_spacing: [2,2] - grid_spacing_unit: microns - optical_channels: - - name: OpticalChannel1 - emission_lambda: 500.0 - description: description - - name: OpticalChannel2 - emission_lambda: 500.0 - description: description - TwoPhotonSeries: - - name: TwoPhotonSeries - description: description diff --git a/metadatafiles/nct_ophys_metafile_suite2p.yaml b/metadatafiles/nct_ophys_metafile_suite2p.yaml deleted file mode 100644 index aab232a6..00000000 --- a/metadatafiles/nct_ophys_metafile_suite2p.yaml +++ /dev/null @@ -1,62 +0,0 @@ ---- -NWBFile: - session_start_time: 2020-02-02 00:00:00 - keywords: [keyword1, keyword2] - experiment_description: My two-photon microscope - session_id: session id goes here - experimenter: [testname] - identifier: nwbfile id - institution: inistitution name - lab: lab name - session_description: ses desc - surgery: surgery description - pharmacology: pharma - protocol: protocol used - related_publications: [pub1, pub2] - notes: nwbfile notes - virus: virus info -Subject: - subject_id: subjectID - description: subject descriptoin - genotype: genotype - sex: F - species: species - weight: weight number - date_of_birth: 2010-02-02 00:00:00 -Ophys: - Device: - - name: Microscope - description: ophys_device1_description - Fluorescence: - name: Fluorescence - roi_response_series: - - name: RoiResponseSeries - description: array of fluorescence traces - - name: Neuropil - description: array of neuropil fluorescence traces - - name: Deconvolved - description: array of deconvolved traces - ImageSegmentation: - name: ABCD - plane_segmentations: - - name: MyplaneSegmentation - description: Segmented ROIs - ImagingPlane: - - description: standard - excitation_lambda: 600.0 - imaging_rate: 1.0 - indicator: GCaMP - location: V1 - name: ImagingPlane - grid_spacing: [2,2] - grid_spacing_unit: microns - optical_channels: - - name: OpticalChannel1 - emission_lambda: 500.0 - description: description - - name: OpticalChannel2 - emission_lambda: 500.0 - description: description - TwoPhotonSeries: - - name: TwoPhotonSeries - description: description diff --git a/metadatafiles/nwbwriter.schema.json b/metadatafiles/nwbwriter.schema.json deleted file mode 100644 index 36453541..00000000 --- a/metadatafiles/nwbwriter.schema.json +++ /dev/null @@ -1,172 +0,0 @@ -{ - "$schema": "http://json-schema.org/draft-07/schema#", - "$id": "ophys_metafile.schema.json", - "title": "Schema for the metafile", - "description": "Schema for the metafile", - "version": "0.1.0", - "type": "object", - "required": ["NWBFile","Subject","ophys"], - "additionalProperties": false, - "properties": { - "NWBFile": { - "type": "object", - "additionalProperties": false, - "required": ["session_start_time", "identifier", "session_description"], - "properties": { - "keywords": { - "description": "Terms to search over", - "type": "array", - "items": {"title": "keyword", "type": "string"} - }, - "experiment_description": {"type": "string", "description": "general description of the experiment"}, - "session_id": {"type": "string", "description": "lab-specific ID for the session"}, - "experimenter": { - "description": "Name of person/people who performed experiment", - "type": "array", - "items": {"type": "string", "title": "experimenter"} - }, - "identifier": {"type": "string", "description": "A unique text identifier for the file. If one is not provided it will be randomly assigned"}, - "institution": {"type": "string", "description": "Institution(s) where experiment is performed"}, - "lab": {"type": "string", "description": "Lab where experiment was performed"}, - "session_description": {"type": "string", "description": "A description of the session where this data was generated"}, - "session_start_time": {"type": "string", "format": "date-time", "description": "The start date and time of the recording session"}, - "surgery": {"type": "string", "description": "Narrative description about surgery/surgeries, including date(s) and who performed surgery."}, - "pharmacology": { - "type": "string", - "description": "Description of drugs used, including how and when they were administered. Anesthesia(s), painkiller(s), etc., plus dosage, concentration, etc." - }, - "protocol": { - "type": "string", - "description": "Experimental protocol, if applicable. E.g., include IACUC protocol" - }, - "related_publications": { - "type": "array", - "items": {"title": "related publication", "type": "string"} - }, - "notes": {"type": "string", "description": "Notes about the experiment."}, - "virus": {"type": "string", "description": "Narrative description about surgery/surgeries, including date(s) and who performed surgery."} - } - }, - "Subject": { - "type": "object", - "required": ["subject_id"], - "properties": { - "description": {"type": "string", "default": "no description", "description": "Description of subject and where subject came from (e.g., breeder, if animal)."}, - "genotype": {"type": "string", "description": "Genetic strain. If absent, assume Wild Type (WT)"}, - "sex": {"type": "string", "enum": ["M", "F", "U", "O"], "default": "U"}, - "species": {"type": "string", "description": "Species of subject. Use latin name."}, - "subject_id": {"type": "string", "description": "ID of animal/person used/participating in experiment (lab convention)"}, - "weight": {"type": "string", "description": "Weight at time of experiment, at time of surgery and at other important times."}, - "date_of_birth": {"type": "string", "format": "date-time", "description": "Date of birth of subject. Can be supplied instead of 'age'."} - } - }, - "ophys": { - "additionalProperties": false, - "type": "object", - "required": ["Device"], - "properties": { - "Device": {"$ref": "#/definitions/Devices"}, - "DfOverF": { - "type": "object", - "required": ["name","roi_response_series"], - "properties": { - "name": {"type": "string", "default": "DfOverF"}, - "roi_response_series": { - "type": "array", - "title": "ROI response series", - "items": {"$ref": "#/definitions/RoiResponseSeries"} - } - } - }, - "Fluorescence": { - "type": "object", - "required": ["name","roi_response_series"], - "properties": { - "name": {"type": "string", "default": "Fluorescence"}, - "roi_response_series": { - "type": "array", - "title": "ROI response series", - "items": {"$ref": "#/definitions/RoiResponseSeries"} - } - } - }, - "ImageSegmentation": { - "type": "object", - "required": ["name", "plane_segmentations"], - "properties": { - "name": {"type": "string"}, - "plane_segmentations": { - "type": "array", - "items": { - "title": "PlaneSegmentation", - "type": "object", - "required": ["name", "description"], - "properties": { - "name": {"type": "string", "default": "PlaneSegmentation"}, - "description": {"type": "string", "default": "Segmented ROIs"} - } - } - } - } - }, - "ImagingPlane": { - "type": "array", - "items": { - "title": "ImagingPlane", - "type": "object", - "required": ["name", "description", "optical_channels"], - "properties": { - "name": {"type": "string", "default": "ImagingPlane"}, - "description": {"type": "string", "description": "An area in the brain where imaging was done"}, - "device": {"type": "string"}, - "excitation_lambda": {"type": "number"}, - "imaging_rate": {"type": "number"}, - "indicator": {"type": "string"}, - "location": {"type": "string"}, - "optical_channels": { - "type": "array", - "items": { - "title": "OpticalChannel", - "type": "object", - "required": ["emission_lambda"], - "properties": { - "name": {"type": "string", "default": "OpticalChannel"}, - "description": {"type": "string"}, - "emission_lambda": {"type": "number"} - } - } - } - } - } - }, - "TwoPhotonSeries": { - "type": "array", - "items": { - "title": "TwoPhotonSeries", - "type": "object", - "required": ["name", "description"], - "properties": { - "name": {"type": "string", "default": "TwoPhotonSeries"}, - "description": {"type": "string"} - } - } - } - } - } - }, - "definitions": { - "TimeSeries": { - "type": "object", "required": ["name", "description"], "properties": { - "name": {"type": "string"}, "description": {"type": "string"}, "conversion": {"type": "number", "default": 1.0}, "starting_time": {"type": "number"}, "resolution": {"type": "number"}, "comments": {"type": "string"} - } - }, "Devices": { - "type": "array", "items": { - "title": "Device", "type": "object", "required": ["name", "description"], "properties": { - "name": {"type": "string", "default": "Device"}, "tag": {"type": "string"}, "description": {"type": "string"} - } - } - }, "RoiResponseSeries": { - "title": "RoiResponseSeries", "type": "object", "allOf": [{"$ref": "#/definitions/TimeSeries"}] - } - } -}