the rest

.gitattributes

@@ -0,0 +1,2 @@
+*.npy filter=lfs diff=lfs merge=lfs -text
+*.dat filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -1,3 +1,6 @@
+# phy
+.phy/
+
 # ---> Python
 # Byte-compiled / optimized / DLL files
 __pycache__/

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

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

expipe.yaml

@@ -0,0 +1 @@
+{database_version: 2, project: septum-mec, type: project}

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],
+      },
+}

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],
+      }
+    }

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

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

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

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

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

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

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

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

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

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

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

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

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.

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.

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

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.

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.

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

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

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: ''

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: ''

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

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

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

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

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

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: ''

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

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

templates/hardware_openephys_optogenetics.yaml

@@ -0,0 +1,3 @@
+registered: '2018-10-25T21:55:28'
+identifier: hardware_openephys_optogenetics
+name: hardware_openephys_optogenetics

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

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: ''

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

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

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.

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.

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.

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

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.

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.

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.

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

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 .

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 .

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.

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