diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 000000000..4f4b5c732 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,2 @@ +*.npy filter=lfs diff=lfs merge=lfs -text +*.dat filter=lfs diff=lfs merge=lfs -text diff --git a/.gitignore b/.gitignore index ccc6eb13a..93c565fe7 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,6 @@ +# phy +.phy/ + # ---> Python # Byte-compiled / optimized / DLL files __pycache__/ diff --git a/entities/1834/attributes.yaml b/entities/1834/attributes.yaml new file mode 100644 index 000000000..388f709cc --- /dev/null +++ b/entities/1834/attributes.yaml @@ -0,0 +1,9 @@ +tags: +- AAV5-EF1a-DIO-hChR2(H134R)-eYFP-FF1 +- pv-cre +location: IMB +registered: '2019-03-19T09:52:11' +datetime: '2019-03-19T09:52:11' +users: +- Charlotte +type: Subject diff --git a/entities/1849/attributes.yaml b/entities/1849/attributes.yaml new file mode 100644 index 000000000..1621df89e --- /dev/null +++ b/entities/1849/attributes.yaml @@ -0,0 +1,9 @@ +tags: +- AAV5-EF1a-DIO-hChR2(H134R)-eYFP-FF1 +- pv-cre +location: IMB +registered: '2019-03-19T10:07:27' +datetime: '2019-03-19T10:07:27' +users: +- Charlotte +type: Subject diff --git a/expipe.yaml b/expipe.yaml new file mode 100755 index 000000000..6749d5468 --- /dev/null +++ b/expipe.yaml @@ -0,0 +1 @@ +{database_version: 2, project: septum-mec, type: project} diff --git a/probes/tetrode_16.prb b/probes/tetrode_16.prb new file mode 100644 index 000000000..c683dc782 --- /dev/null +++ b/probes/tetrode_16.prb @@ -0,0 +1,20 @@ +channel_groups = { + # Tetrode index + 0: + { + 'channels': [0, 1, 2, 3], + }, + 1: + { + 'channels': [4, 5, 6, 7], + }, + 2: + { + + 'channels': [8, 9, 10, 11], + }, + 3: + { + 'channels': [12, 13, 14, 15], + }, +} diff --git a/probes/tetrode_32.prb b/probes/tetrode_32.prb new file mode 100644 index 000000000..8c162d9b9 --- /dev/null +++ b/probes/tetrode_32.prb @@ -0,0 +1,36 @@ +channel_groups = { + # Tetrode index + 0: + { + 'channels': [0, 1, 2, 3], + }, + 1: + { + 'channels': [4, 5, 6, 7], + }, + 2: + { + + 'channels': [8, 9, 10, 11], + }, + 3: + { + 'channels': [12, 13, 14, 15], + }, + 4: + { + 'channels': [16, 17, 18, 19], + }, + 5: + { + 'channels': [20, 21, 22, 23], + }, + 6: + { + 'channels': [24, 25, 26, 27], + }, + 7: + { + 'channels': [28, 29, 30, 31], + } + } diff --git a/scripts/backup_action b/scripts/backup_action new file mode 100755 index 000000000..36a6bbe8b --- /dev/null +++ b/scripts/backup_action @@ -0,0 +1,2 @@ +#!/bin/bash +rsync -rzuP --exclude=.phy actions/$1 nird:/projects/NS9048K/NORSTORE_OSL_DISK/NS9048K/server/septum-mec/actions diff --git a/scripts/fetch_action b/scripts/fetch_action new file mode 100755 index 000000000..760d7d3ff --- /dev/null +++ b/scripts/fetch_action @@ -0,0 +1,2 @@ +#!/bin/bash +rsync -rzv --progress nird:/projects/NS9048K/NORSTORE_OSL_DISK/NS9048K/server/septum-mec/actions/$1 actions diff --git a/scripts/fetch_action_not_yaml b/scripts/fetch_action_not_yaml new file mode 100755 index 000000000..07bb79877 --- /dev/null +++ b/scripts/fetch_action_not_yaml @@ -0,0 +1,2 @@ +#!/bin/bash +rsync -rzv --progress --exclude="*.yaml" nird:/projects/NS9048K/NORSTORE_OSL_DISK/NS9048K/server/septum-mec/actions/$1 actions diff --git a/scripts/fetch_elphys b/scripts/fetch_elphys new file mode 100755 index 000000000..5e6245b31 --- /dev/null +++ b/scripts/fetch_elphys @@ -0,0 +1,2 @@ +#!/bin/bash +rsync -rzv --progress nird:/projects/NS9048K/NORSTORE_OSL_DISK/NS9048K/server/septum-mec/actions/$1/data/main.exdir/processing/electrophysiology actions/$1/data/main.exdir/processing diff --git a/scripts/git_push_batch b/scripts/git_push_batch new file mode 100755 index 000000000..5b5e578a2 --- /dev/null +++ b/scripts/git_push_batch @@ -0,0 +1,7 @@ +#!/bin/bash + +for ((n=$1;n>0;n-=1)) +do + git push origin HEAD~$n:master +done +git push diff --git a/scripts/phy2exdir_all_actions b/scripts/phy2exdir_all_actions new file mode 100755 index 000000000..c6f1d4064 --- /dev/null +++ b/scripts/phy2exdir_all_actions @@ -0,0 +1,5 @@ +#!/bin/bash +for action in 1833-010719-1 1833-010719-2 1833-020719-1 1833-020719-2 1833-020719-3 1833-020719-4 1833-050619-1 1833-050619-2 1833-050619-3 1833-050619-4 1833-060619-1 1833-060619-2 1833-120619-1 1833-120619-2 1833-120619-3 1833-120619-4 1833-200619-1 1833-200619-2 1833-200619-3 1833-200619-4 1833-260619-1 1833-260619-2 1833-260619-3 1833-260619-4 1833-290519-1 1833-290519-2 1833-290519-3 1833-290519-4 1834-010319-1 1834-010319-3 1834-010319-4 1834-010319-5 1834-060319-1 1834-060319-2 1834-060319-3 1834-060319-4 1834-110319-1 1834-110319-2 1834-110319-3 1834-110319-5 1834-110319-6 1834-120319-1 1834-120319-2 1834-120319-3 1834-120319-4 1834-150319-1 1834-150319-2 1834-150319-3 1834-150319-4 1834-220319-1 1834-220319-2 1834-220319-3 1834-220319-4 1834-230219-1 1834-250219-1 1839-060619-1 1839-060619-3 1839-060619-4 1839-060619-5 1839-120619-1 1839-120619-2 1839-120619-3 1839-120619-4 1839-200619-1 1839-200619-2 1839-290519-1 1839-290519-2 1839-290519-3 1849-010319-2 1849-010319-4 1849-010319-5 1849-060319-1 1849-060319-2 1849-060319-3 1849-060319-4 1849-110319-1 1849-110319-2 1849-110319-3 1849-150319-1 1849-150319-2 1849-150319-3 1849-150319-4 1849-220319-2 1849-220319-3 1849-220319-4 1849-220319-5 1849-260219-2 1849-270219-1 1849-280219-1 1849-280219-2 1849-280219-3 1849-280219-4 +do + expipe process phy2exdir $action +done diff --git a/scripts/push_processing b/scripts/push_processing new file mode 100755 index 000000000..9ccfe4341 --- /dev/null +++ b/scripts/push_processing @@ -0,0 +1,3 @@ +#!/bin/bash +rsync -rzuP --exclude=.phy --remove-source-files actions/$1 nird:/projects/NS9048K/NORSTORE_OSL_DISK/NS9048K/server/septum-mec/actions +find actions/ -type d -empty -delete diff --git a/scripts/reset_from_nird b/scripts/reset_from_nird new file mode 100755 index 000000000..451b44709 --- /dev/null +++ b/scripts/reset_from_nird @@ -0,0 +1,5 @@ +#!/bin/bash +for action in 1833-010719-1 1833-010719-2 1833-020719-1 1833-020719-2 1833-020719-3 1833-020719-4 1833-050619-1 1833-050619-2 1833-050619-3 1833-050619-4 1833-060619-1 1833-060619-2 1833-120619-1 1833-120619-2 1833-120619-3 1833-120619-4 1833-200619-1 1833-200619-2 1833-200619-3 1833-200619-4 1833-260619-1 1833-260619-2 1833-260619-3 1833-260619-4 1833-290519-1 1833-290519-2 1833-290519-3 1833-290519-4 1834-010319-1 1834-010319-3 1834-010319-4 1834-010319-5 1834-060319-1 1834-060319-2 1834-060319-3 1834-060319-4 1834-110319-1 1834-110319-2 1834-110319-3 1834-110319-5 1834-110319-6 1834-120319-1 1834-120319-2 1834-120319-3 1834-120319-4 1834-150319-1 1834-150319-2 1834-150319-3 1834-150319-4 1834-220319-1 1834-220319-2 1834-220319-3 1834-220319-4 1834-230219-1 1834-250219-1 1839-060619-1 1839-060619-3 1839-060619-4 1839-060619-5 1839-120619-1 1839-120619-2 1839-120619-3 1839-120619-4 1839-200619-1 1839-200619-2 1839-290519-1 1839-290519-2 1839-290519-3 1849-010319-2 1849-010319-4 1849-010319-5 1849-060319-1 1849-060319-2 1849-060319-3 1849-060319-4 1849-110319-1 1849-110319-2 1849-110319-3 1849-150319-1 1849-150319-2 1849-150319-3 1849-150319-4 1849-220319-2 1849-220319-3 1849-220319-4 1849-220319-5 1849-260219-2 1849-270219-1 1849-280219-1 1849-280219-2 1849-280219-3 1849-280219-4 +do + rsync -rltzv --progress --checksum --ignore-times --exclude="*.yaml" nird:/projects/NS9048K/NORSTORE_OSL_DISK/NS9048K/server/septum-mec/actions/$action actions +done diff --git a/templates/anaesthesia.yaml b/templates/anaesthesia.yaml new file mode 100644 index 000000000..acd9b0647 --- /dev/null +++ b/templates/anaesthesia.yaml @@ -0,0 +1,14 @@ +anaesthetic: + definition: The drug used for anaesthesia. + value: Isoflurane +registered: '2018-10-25T21:55:28' +identifier: anaesthesia +notes: + value: '' +anaesthetic_dose: + definition: The dose of the used anaesthetic. + value: 1 L/M at 1.5 with a small amount of ventilation +description: + definition: A textual description of the preparation. + value: Anaesthetics +name: anaesthesia diff --git a/templates/anaesthesia_ketamine.yaml b/templates/anaesthesia_ketamine.yaml new file mode 100644 index 000000000..ad9ea4303 --- /dev/null +++ b/templates/anaesthesia_ketamine.yaml @@ -0,0 +1,20 @@ +anaesthetic_antidrug: + definition: The drug used to wake up from anaesthesia. + value: Antisedan +anaesthetic: + definition: The drug used for anaesthesia. + value: Ketalar+Domitor +registered: '2018-10-25T21:55:28' +identifier: anaesthesia_ketamine +anaesthetic_dose: + unit: mL + value: '' +notes: + value: '' +anaesthetic_antidrug_dose: + unit: mL + value: 0.1 +description: + definition: A textual description of the preparation. + value: Anaesthetics +name: anaesthesia_ketamine diff --git a/templates/anaesthesia_local.yaml b/templates/anaesthesia_local.yaml new file mode 100644 index 000000000..2ddeb078d --- /dev/null +++ b/templates/anaesthesia_local.yaml @@ -0,0 +1,17 @@ +local_anaesthetic_location: + definition: Describes the place the local anaesthetic was applied. + value: Skin covering dorsal part of head, around cut area. +local_anaesthetic_dose: + unit: mL + value: 0.05 +registered: '2018-10-25T21:55:28' +identifier: anaesthesia_local +notes: + value: '' +local_anaesthetic: + definition: The drug that was used for local anaesthesia. + value: Marcain +description: + definition: A textual description of the preparation. + value: Local anaesthetics +name: anaesthesia_local diff --git a/templates/analgesia.yaml b/templates/analgesia.yaml new file mode 100644 index 000000000..de91463ed --- /dev/null +++ b/templates/analgesia.yaml @@ -0,0 +1,15 @@ +registered: '2018-10-25T21:55:28' +identifier: analgesia +analgesic_dose: + unit: mL + value: 0.2 +notes: + value: '' +definition: Analgesia , during surgery. +description: + definition: A textual description of the preparation. + value: Analgesics +name: analgesia +analgesic: + definition: The drug used for analgesia. + value: Temgesic diff --git a/templates/analgesia_post.yaml b/templates/analgesia_post.yaml new file mode 100644 index 000000000..f2253d439 --- /dev/null +++ b/templates/analgesia_post.yaml @@ -0,0 +1,18 @@ +post_op_analgesic: + definition: The drug used for post surgery analgesia. + value: Rimadyl +registered: '2018-10-25T21:55:28' +identifier: analgesia_post +notes: + value: '' +post_op_analgesic_procedure: + definition: The procedure of post surgery analgesic. + value: Rimadyl was given in equal doses for 3 consecutive days after surgery +post_op_analgesic_dose: + unit: mL + value: 0.5 +description: + definition: A textual description of the preparation. + value: Analgesics +name: analgesia_post +definition: Analgesia , e.g. post surgery. diff --git a/templates/behavior.yaml b/templates/behavior.yaml new file mode 100644 index 000000000..6adb82a1c --- /dev/null +++ b/templates/behavior.yaml @@ -0,0 +1,27 @@ +registered: '2018-10-25T21:55:28' +identifier: behavior +notes: + value: '' +environment: + definition: The environment in which the experiments were conducted. Classical environments + are e.g. the Y-maze or T-maze. Some environments are called enriched also reduced + or even natural. + value: Open field +protocol_info: + definition: Additional information to the task protocol undertaken by the subject. + value: 'Weetabix Weetos choco: 41 % fullkornshvete, sukker, hvetemel, maltodekstrin, + kakaopulver, rapsolje, melkepulver, salt, E508, aroma, Energi: 392 kcal/1656 kJ, + Protein: 8 g, Karbohydrater: 76 g, hvorav sukkerarter: 29 g, Fett: 4,9 g, Herav + mettede fettsyrer: 1,0 g, Kostfiber: 5,8 g, Natrium: 0,09 g' +paradigm: + definition: The paradigm used in the experiment, e.g. Learning, navigation, etc... + value: navigation +individual_count: + definition: The number of individuals that are observed/investigated at the same + time. + value: 1 +protocol: + definition: A description of the task protocol undertaken by the subject. + value: foraging for Weetos +name: behavior +definition: Describing the type of behavior that was assesed in experimental setup. diff --git a/templates/drive_depth_adjustment.yaml b/templates/drive_depth_adjustment.yaml new file mode 100644 index 000000000..8e44ada32 --- /dev/null +++ b/templates/drive_depth_adjustment.yaml @@ -0,0 +1,15 @@ +adjustment: + unit: um + value: '' +registered: '2018-10-25T21:55:28' +depth: + unit: mm + value: '' +notes: + value: '' +experimenter: '' +date: dd.mm.yyyy:HH:MM +identifier: drive_depth_adjustment +location: Left, Right +name: drive_depth_adjustment +definition: Adjustment length of drive diff --git a/templates/environment_open_field_tracking.yaml b/templates/environment_open_field_tracking.yaml new file mode 100644 index 000000000..4eb5b0d48 --- /dev/null +++ b/templates/environment_open_field_tracking.yaml @@ -0,0 +1,45 @@ +box_local_que_position: + definition: Position of local que in the environment, relative to position reference + value: north +box_distal_que: + definition: Distal que in the environment. + value: curtains, DAC, cable to headstage in celing +light_intensity: + definition: Intesity of light + value: minimal light from small lamp and desktop computer screen +notes: + value: '' +box_type: + definition: The shape of the box + value: square box +box_size: + unit: cm + value: + - 100.0 + - 100.0 +position_reference: + definition: Position reference of the room + value: TODO +registered: '2018-10-25T21:55:28' +identifier: environment_open_field_tracking +room_temperature: + uncertainty: 0.1 + unit: degC + value: 21.0 +experimenter_position: + definition: Position of experimenter relative to behaviour setup + value: right side +relative_humidity: + uncertainty: 10 + unit: '%' + value: 55.0 +box_distal_que_position: + definition: Distal que in the environment + value: north +box_local_que: + definition: Local que in the environment + value: white A4 paper sheet +description: + value: Environment during open field experiment. +name: environment_open_field_tracking +definition: Describing tracking setup, e.g. info on box size and ques. diff --git a/templates/environment_rat_housing.yaml b/templates/environment_rat_housing.yaml new file mode 100644 index 000000000..3b69be598 --- /dev/null +++ b/templates/environment_rat_housing.yaml @@ -0,0 +1,26 @@ +ventilation: + definition: Ventilation rate. + value: 5 - 20 pr. hour. +air_humidity: + unit: '%' + value: + - 55 +- 10 +light_intensity: + definition: Intesity of light during light phase. + value: '> 100 lux' +notes: + value: '' +registered: '2018-10-25T21:55:28' +light_cycle: + definition: The time when is swiched on and off. + value: 10:00 p.m. - 10:00 a.m. +name: environment_rat_housing +light_cycle_duration: + definition: The duration with light on. + value: 12 hours +identifier: environment_rat_housing +description: + value: Housing environment. +room_temperature: + value: '' +definition: Describing the housing environment of the housing. diff --git a/templates/environment_surgery_station.yaml b/templates/environment_surgery_station.yaml new file mode 100644 index 000000000..80e7dbc6e --- /dev/null +++ b/templates/environment_surgery_station.yaml @@ -0,0 +1,4 @@ +registered: '2018-10-25T21:55:28' +identifier: environment_surgery_station +name: environment_surgery_station +todo: todo diff --git a/templates/hardware_axona_camera_objective.yaml b/templates/hardware_axona_camera_objective.yaml new file mode 100644 index 000000000..49c4bca1e --- /dev/null +++ b/templates/hardware_axona_camera_objective.yaml @@ -0,0 +1,62 @@ +registered: '2018-10-25T21:55:28' +aperture: + unit: dimensionless + value: '' +notes: + value: '' +focal_length_range: + unit: dimensionless + value: '' +transmission_lower_bound: + unit: dimensionless + value: '' +transmission_upper_bound: + unit: dimensionless + value: '' +model: + definition: The objective model name. + value: '' +maximum_aperture: + unit: dimensionless + value: '' +manufacturer: + definition: The Manufacturer providing the objective. + value: '' +inventory_no: + definition: The inventory number of this device. + value: '' +name: hardware_axona_camera_objective +transmission_range: + unit: dimensionless + value: '' +type: + alternatives: + - FixedApperture + - FixedFocus + - Macro + - Zoom + definition: The type of objective. + value: '' +identifier: hardware_axona_camera_objective +owner: + definition: The owner of this device. + value: '' +serial_no: + definition: The serial number of this device. + value: '' +numerical_aperture: + unit: dimensionless + value: '' +mount: + alternatives: + - C-Mount + - CS-Mount + definition: The type of mount. + value: '' +description: + definition: A description of this hardware item. + value: '' +focal_length: + unit: dimensionless + value: '' +definition: Describing the objective used on the tracking camera diff --git a/templates/hardware_axona_daq.yaml b/templates/hardware_axona_daq.yaml new file mode 100644 index 000000000..7f58afa78 --- /dev/null +++ b/templates/hardware_axona_daq.yaml @@ -0,0 +1,52 @@ +sample_rate: + definition: The sample rate with which an individual input channel was sampled. + Given in Hz. + value: '48000' +registered: '2018-10-25T21:55:28' +notes: + value: '' +polarity: + definition: The polarity of the measurement "unipolar" or "bipolar". + value: '' +channel_count: + definition: The number of input channels of the DAQ-device. + value: '64' +manufacturer: + definition: The Manufacturer of this hardware item. + value: Axona +reference: + definition: The reference to which voltages were measured. Usually either "common + ground" or "differential". + value: differential +inventory_no: + definition: The inventory number of the device. + value: '' +dio_line_count: + definition: The number of digital input/output lines (DIO) of the device. + value: '' +model: + definition: The model name of this hardware item. + value: '' +identifier: hardware_axona_daq +owner: + definition: Who's the owner of the device. + value: Marianne Fyhn, Torkel Hafting +max_sample_rate: + unit: Hz + value: + - 48000.0 +used_channel_count: + definition: The number of used analog input channels. + value: '32' +serial_no: + definition: The device's serial number. + value: '' +definition: Describing the Axonda DAC +description: + definition: A description of this hardware item. + value: '' +name: hardware_axona_daq +resolution: + definition: The voltage resolution of the analog input (AIN) subsystem given in + bit. + value: '' diff --git a/templates/hardware_axona_optogenetics.yaml b/templates/hardware_axona_optogenetics.yaml new file mode 100644 index 000000000..b89abb5a3 --- /dev/null +++ b/templates/hardware_axona_optogenetics.yaml @@ -0,0 +1,19 @@ +channels: + definition: The used analog input channels for ttl pulses. + value: + - 33.0 + - 34.0 + - 35.0 + - 36.0 +identifier: hardware_axona_optogenetics +registered: '2018-10-25T21:55:28' +notes: + value: '' +definition: Optogenetics when combined with the Axona recording system +tetrode: + definition: The used analog input tetrode for ttl pulses. + value: '9' +name: hardware_axona_optogenetics +description: + definition: A description of this hardware item. + value: '' diff --git a/templates/hardware_axona_tracker.yaml b/templates/hardware_axona_tracker.yaml new file mode 100644 index 000000000..74653c6fc --- /dev/null +++ b/templates/hardware_axona_tracker.yaml @@ -0,0 +1,36 @@ +sample_rate: + unit: Hz + value: '' +registered: '2018-10-25T21:55:28' +calibration: + definition: The calibration procedure. + value: '' +notes: + value: '' +manufacturer: + definition: The Manufacturer of this hardware item. + value: '' +inventory_no: + definition: The inventory number of the device. + value: '' +model: + definition: The model name of this hardware item. + value: '' +filter: + definition: The kind of filter applied to the data. + value: '' +owner: + definition: Who's the owner of the device. + value: '' +identifier: hardware_axona_tracker +serial_no: + definition: The device's serial number. + value: '' +comment: + definition: Space for some comments. + value: '' +description: + definition: A description of this hardware item. + value: '' +name: hardware_axona_tracker +definition: Describing the tracking setup with Axona diff --git a/templates/hardware_blue_laser.yaml b/templates/hardware_blue_laser.yaml new file mode 100644 index 000000000..a784faed7 --- /dev/null +++ b/templates/hardware_blue_laser.yaml @@ -0,0 +1,4 @@ +registered: '2018-10-25T21:55:28' +identifier: hardware_blue_laser +name: hardware_blue_laser +todo: todo diff --git a/templates/hardware_intan_headstage.yaml b/templates/hardware_intan_headstage.yaml new file mode 100644 index 000000000..0a70452aa --- /dev/null +++ b/templates/hardware_intan_headstage.yaml @@ -0,0 +1,31 @@ +name: hardware_intan_headstage +definition: This is a generic hardware section meant to take information of items + for which no specific terminology exists. +type: + definition: The type of amplifier. E.g. extracellular, intracellular amplifier etc. + value: extracellular +identifier: hardware_intan_headstage +registered: '2018-10-25T21:55:28' +serial_no: + definition: The device's serial number. + value: '' +model: + alternatives: + - RHD2116 + - RHD2132 + - RHS2116 + - RHS2132 + definition: The model name of this hardware item. + value: '' +manufacturer: + definition: The Manufacturer of this hardware item. + value: Intan +description: + definition: A description of this hardware item. + value: Headstage +inventory_no: + definition: The inventory number of the device. + value: '' +owner: + definition: Who's the owner of the device. + value: Fyhn-Hafting diff --git a/templates/hardware_laser_device.yaml b/templates/hardware_laser_device.yaml new file mode 100644 index 000000000..6707d9ed5 --- /dev/null +++ b/templates/hardware_laser_device.yaml @@ -0,0 +1,4 @@ +TODO: TODO +registered: '2018-10-25T21:55:28' +identifier: hardware_laser_device +name: hardware_laser_device diff --git a/templates/hardware_laser_measure_device.yaml b/templates/hardware_laser_measure_device.yaml new file mode 100644 index 000000000..137b7066c --- /dev/null +++ b/templates/hardware_laser_measure_device.yaml @@ -0,0 +1,4 @@ +TODO: TODO +registered: '2018-10-25T21:55:28' +identifier: hardware_laser_measure_device +name: hardware_laser_measure_device diff --git a/templates/hardware_laser_settings.yaml b/templates/hardware_laser_settings.yaml new file mode 100644 index 000000000..56447c76a --- /dev/null +++ b/templates/hardware_laser_settings.yaml @@ -0,0 +1,25 @@ +setting: + definition: The actual manual laser intensity setting. + value: '' +intensity: + uncertainty: '' + unit: '' + measure_device: '' + value: '' +registered: '2018-10-25T21:55:28' +identifier: hardware_laser_settings +intensity_date_time: + value: '' +intensity_file_url: + definition: The URL of a file containing the intensity measure. OBLIGATORY + value: '' +laser_device: + definition: The hardware generating the laser pulse. + value: blue laser +wavelength: + unit: nm + value: + - 473.0 +name: hardware_laser_settings +intensity_info: + value: '' diff --git a/templates/hardware_microdrive_optetrode.yaml b/templates/hardware_microdrive_optetrode.yaml new file mode 100644 index 000000000..0a3cffaa1 --- /dev/null +++ b/templates/hardware_microdrive_optetrode.yaml @@ -0,0 +1,4 @@ +registered: '2018-10-25T21:55:28' +identifier: hardware_microdrive_optetrode +name: hardware_microdrive_optetrode +todo: todo diff --git a/templates/hardware_openephys_daq.yaml b/templates/hardware_openephys_daq.yaml new file mode 100644 index 000000000..00f63549d --- /dev/null +++ b/templates/hardware_openephys_daq.yaml @@ -0,0 +1,26 @@ +name: hardware_openephys_daq +definition: This is a generic hardware section meant to take information of items + for which no specific terminology exists. +type: + definition: The type of amplifier. E.g. extracellular, intracellular amplifier etc. + value: extracellular +identifier: hardware_openephys_daq +registered: '2018-10-25T21:55:28' +serial_no: + definition: The device's serial number. + value: '' +model: + definition: The model name of this hardware item. + value: XEM6010 Xilinx Spartan-6 FPGA +manufacturer: + definition: The Manufacturer of this hardware item. + value: Open-Ephys +description: + definition: A description of this hardware item. + value: Open-Ephys Acquisition System +inventory_no: + definition: The inventory number of the device. + value: '' +owner: + definition: Who's the owner of the device. + value: Fyhn-Hafting diff --git a/templates/hardware_openephys_optogenetics.yaml b/templates/hardware_openephys_optogenetics.yaml new file mode 100644 index 000000000..e24e3587c --- /dev/null +++ b/templates/hardware_openephys_optogenetics.yaml @@ -0,0 +1,3 @@ +registered: '2018-10-25T21:55:28' +identifier: hardware_openephys_optogenetics +name: hardware_openephys_optogenetics diff --git a/templates/hardware_optic_fibre.yaml b/templates/hardware_optic_fibre.yaml new file mode 100644 index 000000000..cefb6a46e --- /dev/null +++ b/templates/hardware_optic_fibre.yaml @@ -0,0 +1,4 @@ +registered: '2018-10-25T21:55:28' +identifier: hardware_optic_fibre +name: hardware_optic_fibre +todo: todo diff --git a/templates/hardware_pointgrey_camera_objective.yaml b/templates/hardware_pointgrey_camera_objective.yaml new file mode 100644 index 000000000..65c2ca894 --- /dev/null +++ b/templates/hardware_pointgrey_camera_objective.yaml @@ -0,0 +1,60 @@ +mount: + alternatives: + - C-Mount + - CS-Mount + definition: The type of mount. + value: '' +registered: '2018-10-25T21:55:28' +aperture: + definition: The actual aperture setting of the objective. + value: '' +focal_length_range: + definition: The range of focal lengths of the objective. + value: '' +transmission_lower_bound: + definition: The lower bound of transmission. + value: '' +transmission_upper_bound: + definition: The upper bound of transmission. + value: '' +model: + definition: The objective model name. + value: '' +manufacturer: + definition: The Manufacturer providing the objective. + value: PointGrey +focal_length: + definition: The focal length of the objective. + value: '' +inventory_no: + definition: The inventory number of this device. + value: '' +transmission_range: + definition: The transmission range (min - max). + value: '' +type: + alternatives: + - FixedApperture + - FixedFocus + - Macro + - Zoom + definition: The type of objective. + value: '' +identifier: hardware_pointgrey_camera_objective +owner: + definition: The owner of this device. + value: '' +serial_no: + definition: The serial number of this device. + value: '' +numerical_aperture: + definition: The numerical aperture (N.A.) of the objective. + value: '' +definition: This section contains properties that describe a camera objective. +description: + definition: A description of this hardware item. + value: '' +name: hardware_pointgrey_camera_objective +maximum_aperture: + definition: The maximum aperture of the objective. + value: '' diff --git a/templates/hardware_pulse_pal.yaml b/templates/hardware_pulse_pal.yaml new file mode 100644 index 000000000..9898b8360 --- /dev/null +++ b/templates/hardware_pulse_pal.yaml @@ -0,0 +1,37 @@ +registered: '2018-10-25T21:55:28' +manufacturer_email: + definition: The Manufacturer's email of this hardware item. + value: sanders@dandrite.au.dk +notes: + value: '' +channel_count: + definition: The number of input channels of the DAQ-device. + value: '4' +manufacturer: + definition: The Manufacturer of this hardware item. + value: Sanworks +inventory_no: + definition: The inventory number of the device. + value: '' +model: + definition: The model name of this hardware item. + value: pulse pal version 1 +identifier: hardware_pulse_pal +owner: + definition: Who's the owner of the device. + value: Marianne Fyhn, Torkel Hafting +used_channel_count: + definition: The number of used analog input channels. + value: '2' +serial_no: + definition: The device's serial number. + value: '' +definition: Describing the Pulse Pal TTL pulse giver hardware. +description: + definition: A description of this hardware item. + value: Pulse Pal is an open source device that generates precise sequences of voltage + pulses. +name: hardware_pulse_pal +polarity: + definition: The polarity of the measurement "unipolar" or "bipolar". + value: unipolar diff --git a/templates/hardware_tetrode.yaml b/templates/hardware_tetrode.yaml new file mode 100644 index 000000000..a8e8c4e9c --- /dev/null +++ b/templates/hardware_tetrode.yaml @@ -0,0 +1,54 @@ +usage: + alternatives: + - Channel + - Ground + - Reference + definition: Usage of tetrode. + value: Channel +registered: '2018-10-25T21:55:28' +notes: + value: '' +material: + definition: The Material the electrodes are made of e.g. glass. tungsten, steel + ... + value: 10 % platinum, 90 % iridium +manufacturer: + definition: The manufacturer of the electrodes if e.g. ordered from a company. + value: California fine wire, CA, USA +impedance: + uncertainty: '100' + value: + - 150.0 + definition: Electrode impedance. + unit: k ohm +coating: + definition: The coating used to insulate the electrodes. + value: Heavy poly-imid +type: + alternatives: + - extracellular + - multi-electrode-array + - multibarrel + - patch + - sharp + definition: The type of electrode registration. + value: extracellular +identifier: hardware_tetrode +electrode_specification: + unit: um + value: + - 17.0 +description: + value: Tetrode - four electrodes wined together. +tip_size: + unit: um + value: + - 34.0 +definition: Describing electrodes in tetrodes used. +electro_plating: + definition: Specifies whether or not electro plating was performed. + value: 'true' +name: hardware_tetrode +electrode_count: + definition: Number of electrodes in a multi-electrode-array. + value: 4 diff --git a/templates/implant_drive_mecl.yaml b/templates/implant_drive_mecl.yaml new file mode 100644 index 000000000..fd6dcae55 --- /dev/null +++ b/templates/implant_drive_mecl.yaml @@ -0,0 +1,80 @@ +angle: + unit: deg + value: 15.0 +registered: '2018-10-25T21:55:28' +notes: + value: Indexes refer to x,y,z respectively, all tetrodes have the same position. +position: + unit: mm + value: + - x + - y + - z +position_reference: + alternatives: + - bregma + - dura + - lambda + - longitudinal suture + - skull + - transverse sinus + definition: By default position are specified by the coordinates of skull. Use this + property for other definitions. + value: + y: transverse sinus + x: lambda + z: dura +description: + value: Implantation of optetrodes in Medial Entorhinal Cortex and fibre optcis in + Medial Septum. +electrophysiology: + channel_groups: + definition: Which channel groups are associated with this electrophysiological + measurement + value: + - 0.0 + - 1.0 + - 2.0 + - 3.0 + type: + alternatives: + - EEG + - EKG + - EMG + - ERG + - extracellular recording + - intracellular recording + - loose patch + - patch clamp + - whole cell patch + value: extracellular recording + ref_electrode_location: + alternatives: + - Anterior to bregma + definition: Describes the location of the reference electrode. + value: Anterior to bregma, left hemisphere + definition: Describing electrophysiology in the expirimental setup. + subtype: + alternatives: + - dual electrode recording + - multi electrode recording + - single electrode recording + definition: Subtype of this electrophysiological experiment. + value: multi electrode recording +identifier: implant_drive_mecl +hemisphere: + alternatives: + C, center: between hemispheres + L, left: left hemisphere + R, right: right hemisphere + value: L +location: + alternatives: + - MECL + - MECR + - MS + definition: 'Describes the brain area of recording. MS: Medial Septum, MECR: Medial + Entorhinal Cortex Right hemisphere, MECL: Medial Entorhinal Cortex Left hemisphere, ' + value: MECL +name: implant_drive_mecl +definition: Describing an implantation procedure of a micro drive. diff --git a/templates/implant_drive_mecr.yaml b/templates/implant_drive_mecr.yaml new file mode 100644 index 000000000..59372ac2e --- /dev/null +++ b/templates/implant_drive_mecr.yaml @@ -0,0 +1,80 @@ +angle: + unit: deg + value: 15.0 +registered: '2018-10-25T21:55:28' +notes: + value: Indexes refer to x,y,z respectively, all tetrodes have the same position. +position: + unit: mm + value: + - x + - y + - z +position_reference: + alternatives: + - bregma + - dura + - lambda + - longitudinal suture + - skull + - transverse sinus + definition: By default position are specified by the coordinates of skull. Use this + property for other definitions. + value: + y: transverse sinus + x: lambda + z: dura +description: + value: Implantation of optetrodes in Medial Entorhinal Cortex and fibre optcis in + Medial Septum. +electrophysiology: + channel_groups: + definition: Which channel groups are associated with this electrophysiological + procedure + value: + - 4.0 + - 5.0 + - 6.0 + - 7.0 + type: + alternatives: + - EEG + - EKG + - EMG + - ERG + - extracellular recording + - intracellular recording + - loose patch + - patch clamp + - whole cell patch + value: extracellular recording + ref_electrode_location: + alternatives: + - Posterior to bregma + definition: Describes the location of the reference electrode. + value: Posterior to bregma, right hemisphere + definition: Describing electrophysiology in the expirimental setup. + subtype: + alternatives: + - dual electrode recording + - multi electrode recording + - single electrode recording + definition: Subtype of this electrophysiological experiment. + value: multi electrode recording +identifier: implant_drive_mecr +hemisphere: + alternatives: + C, center: between hemispheres + L, left: left hemisphere + R, right: right hemisphere + value: R +location: + alternatives: + - MECL + - MECR + - MS + definition: 'Describes the brain area of recording. MS: Medial Septum, MECR: Medial + Entorhinal Cortex Right hemisphere, MECL: Medial Entorhinal Cortex Left hemisphere, ' + value: MECR +name: implant_drive_mecr +definition: Describing an implantation procedure of a micro drive. diff --git a/templates/implant_fibre_ms.yaml b/templates/implant_fibre_ms.yaml new file mode 100644 index 000000000..c9f6afc89 --- /dev/null +++ b/templates/implant_fibre_ms.yaml @@ -0,0 +1,46 @@ +angle: + unit: deg + value: + - 0.0 +hemisphere: + alternatives: + C, center: between hemispheres + L, left: left hemisphere + R, right: right hemisphere + value: C +registered: '2018-10-25T21:55:28' +identifier: implant_fibre_ms +location: + alternatives: + - MECL + - MECR + - MS + definition: 'Describes the brain area of recording. MS: Medial Septum, MECR: Medial + Entorhinal Cortex Right hemisphere, MECL: Medial Entorhinal Cortex Left hemisphere, ' + value: MS +notes: + value: '' +position: + unit: mm + value: + - '0.0' + - '0.6' + - ' z' +position_reference: + alternatives: + - bregma + - dura + - lambda + - longitudinal suture + - skull + - transverse sinus + definition: By default position are specified by the coordinates of skull. Use this + property for other definitions. + value: + - bregma + - ' bregma' + - ' skull' +description: + value: '' +name: implant_fibre_ms +definition: Describing an implantation procedure of an optic fibre. diff --git a/templates/injection_ms.yaml b/templates/injection_ms.yaml new file mode 100644 index 000000000..241f2f8aa --- /dev/null +++ b/templates/injection_ms.yaml @@ -0,0 +1,80 @@ +angle: + unit: deg + value: + - 0.0 +hemisphere: + alternatives: + C, center: between hemispheres + L, left: left hemisphere + R, right: right hemisphere + value: C +syringe_manufacturer: + definition: The manufacturer of the syringe. + value: Hamilton +notes: + value: 1 minute waiting before injection, 8 minute waiting after +flow: + unit: ul/min + definition: The angle of the implant, assuming leveled bregma and lambda, 0 degrees + is vertical implantation + value: + - 0.05 +injection_substance_manufacurer: + definition: Name of manufacturer of the injection substance. + value: Deisseroth lab +position: + unit: mm + value: + - x + - y + - z +position_reference: + alternatives: + - bregma + - dura + - lambda + - longitudinal suture + - skull + - transverse sinus + definition: By default position are specified by the coordinates of skull. Use this + property for other definitions. + value: + y: bregma + x: bregma + z: skull +injection_substance: + definition: The full name of the injection substance, e.g. AAV8-hSyn-eChR2(H134R)-EYFP. + local_marker: '' + value: '' +injection_substance_storage_manufactuer: + definition: Manufacturer of storage device for injection substance + value: '' +injection_substance_information: + definition: Additional information to injection substance. + value: Diluted to 5X10e12 with ice cold PBS (sterile lab PBS +injection_substance_storage_temp: + unit: degC + value: + - -80.0 +identifier: injection_ms +registered: '2018-10-25T21:55:28' +description: + definition: A textual description of the preparation. + value: Injection of virus in medial septum, AAV-mediated expression of channelrhodopsin-2 +location: + alternatives: + - MECL + - MECR + - MS + definition: 'Describes the brain area of recording. MS: Medial Septum, MECR: Medial + Entorhinal Cortex Right hemisphere, MECL: Medial Entorhinal Cortex Left hemisphere, ' + value: MS +definition: Describing an injection procedure e.g. injection of virus. +injection_substance_storage_info: + definition: Information of storage procedure of injection substance. + value: Kept on ice in fridge during surgery, for 2 h +name: injection_ms +syringe_needle_diameter: + unit: um + value: + - 100.0 diff --git a/templates/optic_fibre.yaml b/templates/optic_fibre.yaml new file mode 100644 index 000000000..5146d785d --- /dev/null +++ b/templates/optic_fibre.yaml @@ -0,0 +1,20 @@ +optic_fibre_description: + definition: Description of the optic fibre. + value: Uncleaved Fiber Optic Cannula, Ø2.5 mm Stainless Ferrule, Ø200 µm Core, 0.39 + NA, 20 Pack +registered: '2018-10-25T21:55:28' +identifier: optic_fibre +name: optic_fibre +notes: + value: '' +optic_fibre_diameter: + unit: um + value: + - 200.0 +optic_fibre_serial_num: + definition: The serial number of the optic fibre. + value: CFM12U-20 +optic_fibre_manufacturer: + definition: The manufacturer of the optic fibre. + value: Thor labs +definition: Describing an optic fibre used for optogenetics. diff --git a/templates/optogenetics_anatomical_location.yaml b/templates/optogenetics_anatomical_location.yaml new file mode 100644 index 000000000..7b234f9c3 --- /dev/null +++ b/templates/optogenetics_anatomical_location.yaml @@ -0,0 +1,15 @@ +registered: '2018-10-25T21:55:28' +identifier: optogenetics_anatomical_location +notes: + definition: Notes specific for this stimulus session. + value: '' +location: + alternatives: + MECR: Medial Entorhinal Cortex right hemisphere + MS: Medial Septum + MECL: Medial Entorhinal Cortex left hemisphere + definition: Describes the site of the stimulus application. If the location is MEC, + the depth is the same as in electrophysiology minus 0.5 mm + value: '' +name: optogenetics_anatomical_location +definition: Describing the anatomical location of optogenetic stimulus. diff --git a/templates/optogenetics_paradigm.yaml b/templates/optogenetics_paradigm.yaml new file mode 100644 index 000000000..e87d074a1 --- /dev/null +++ b/templates/optogenetics_paradigm.yaml @@ -0,0 +1,13 @@ +registered: '2018-10-25T21:55:28' +stimulus_type: + alternatives: + positional: Stimulus is activated when subject enters a defined spatial area + train: Multiple trains of set duration and number of pulses + definition: The type of stimulus. + value: '' +notes: + definition: Notes specific for this stimulus session. + value: '' +identifier: optogenetics_paradigm +name: optogenetics_paradigm +definition: Describing the stimulus paradigm for optogenetic stimulus. diff --git a/templates/perfusion_procedure.yaml b/templates/perfusion_procedure.yaml new file mode 100644 index 000000000..8e6004a66 --- /dev/null +++ b/templates/perfusion_procedure.yaml @@ -0,0 +1,36 @@ +time_post_fixative: + unit: h + value: '' +registered: '2018-10-25T21:55:28' +notes: + value: '' +time_stiffness: + unit: min + value: '' +time_liver_clearing: + unit: min + value: '' +flow_rate: + unit: L/min + value: '' +time_true_fixation: + unit: min + value: '' +anaesthetic: + definition: The drug used for anaesthesia. + value: Isoflurane and Pentobarbital +identifier: perfusion_procedure +anaesthetic_dose: + definition: The dose of the used anaesthetic. + value: 1 L/M of Isoflurane until unconcious, then 0.7 mL Pentobarbital +fixative: + definition: The fluid used to fixate the tissue. + value: 4 % paraformaldehyde +buffer: + definition: The fluid used to flush out blood vessels. + value: 0.9 % NaCl in H2O +description: + definition: A textual description of the preparation. + value: Deeply anesthetized animal is perfused in order to preserve brain tissue + for imunohistochemical analysis. +name: perfusion_procedure diff --git a/templates/software_bonsai_gui.yaml b/templates/software_bonsai_gui.yaml new file mode 100644 index 000000000..b02004098 --- /dev/null +++ b/templates/software_bonsai_gui.yaml @@ -0,0 +1,36 @@ +registered: '2018-10-25T21:55:28' +licence_duration: + definition: Duration of the licence for the software. + value: '' +licence_start: + definition: The start date of time limited licence. + value: '' +licence_count: + definition: Number of the software's licence. + value: '' +licence_expiration: + definition: The end date of time limited licence. + value: '' +version: + definition: Version of the software. + value: 2.3.0 +identifier: software_bonsai_gui +owner: + definition: The owner of the software. + value: '' +developer: + definition: The developer or the developers firm. + value: Gonçalo Lopes at the Champalimaud Centre for the Unknown +licence: + definition: License type + value: '' +distribution: + definition: Distribution type + value: '' +description: + definition: The descrisption of the software. + value: Bonsai is open-source software for processing heterogeneous streams of data. + It is ideal for real-time video analysis, but it can simultaneously control your + experiments and/or acquire data from the Open Ephys acquisition board. +name: software_bonsai_gui +definition: This is a software section . diff --git a/templates/software_openephys_gui.yaml b/templates/software_openephys_gui.yaml new file mode 100644 index 000000000..53734fbaf --- /dev/null +++ b/templates/software_openephys_gui.yaml @@ -0,0 +1,36 @@ +registered: '2018-10-25T21:55:28' +licence_duration: + definition: Duration of the licence for the software. + value: '' +licence_start: + definition: The start date of time limited licence. + value: '' +licence_count: + definition: Number of the software's licence. + value: '' +licence_expiration: + definition: The end date of time limited licence. + value: '' +version: + definition: Version of the software. + value: 0.4.1 +identifier: software_openephys_gui +owner: + definition: The owner of the software. + value: '' +developer: + definition: The developer or the developers firm. + value: Open Ephys Team +licence: + definition: License type + value: '' +distribution: + definition: Distribution type + value: '' +description: + definition: The descrisption of the software. + value: The Open Ephys GUI was built by neuroscientists, for neuroscientists. It + already has all the features needed to acquire and visualize your data—but it + also makes it easy to add new modules written in C++. +name: software_openephys_gui +definition: This is a software section . diff --git a/templates/software_pulse_pal_settings.yaml b/templates/software_pulse_pal_settings.yaml new file mode 100644 index 000000000..0287cfeab --- /dev/null +++ b/templates/software_pulse_pal_settings.yaml @@ -0,0 +1,54 @@ +pulse_frequency: + unit: Hz + value: '' +registered: '2018-10-25T21:55:28' +output_device: + definition: The physical output device. + value: Pulse Pal +notes: + definition: Notes specific for this stimulus session. + value: '' +stimulus_file_url: + definition: The URL of a an applied stimulus file. OBLIGATORY + value: '' +repetitions: + definition: The number of repetitions of the described stimulation. Defined as on + time of a train of pulses + value: '' +train_durations: + unit: s + value: '' +pulse_phase_duration: + unit: ms + value: '' +pulse_period: + unit: ms + value: '' +trigger_software: + alternatives: + OpenEphys: Trigger software from the Open Ephys GUI + Matlab: Matlab software provided by PulsePal + definition: What software triggers the pulsepal. + value: '' +output_channels: + definition: The physical output channels used. + value: + - 1.0 + - 2.0 +start_times: + unit: s + value: '' +interstimulus_interval: + unit: s + value: '' +identifier: software_pulse_pal_settings +outputs_to: + definition: The recieving end of the output channels. + value: + - Laser + - ' Acquisition system' +trigger_channels: + definition: If externally triggered, by which channel. + value: '' +name: software_pulse_pal_settings +definition: Describing the settings on pulse pal. diff --git a/templates/subject.yaml b/templates/subject.yaml new file mode 100644 index 000000000..a79a7ecb7 --- /dev/null +++ b/templates/subject.yaml @@ -0,0 +1,46 @@ +label: + definition: If the subject has been labled in a specific way. The lable can be described + here. + value: '' +gender: + definition: Male or female? + value: Male +definition: Describing the subject. +genus: + definition: The Genus of the studied subject. + value: Rattus +notes: + value: '' +health_status: + definition: Information about the health status of this subject. + value: Healthy +birthday: + definition: The birthday. Age can be inferred from the date of recording. + value: dd.mm.yyyy:HH:MM +developmental_stage: + definition: The developemtal stage of the subject. E.g. 'embroyonal', 'adult', 'larval' + etc. + value: adult +registered: '2018-10-25T21:55:28' +identifier: subject +strain: + definition: The strain the subject was taken from. E.g. a specific genetic variation + etc. + value: Long Evans +cell_line: + definition: Cell line of the subject. + value: '' +population: + definition: The population this subject is offspring of. This may be the bee hive, + the ant colony, etc. + value: locally bred +species: + definition: The scientific name of the species e.g. Apis mellifera, Homo sapiens. + value: Rattus norvegicus +weight: + unit: g + value: '' +name: subject +trivial_name: + definition: The trivial name of the species like Honeybee, Human. + value: Rat