This commit is contained in:
Mikkel Elle Lepperød 2019-10-08 16:00:28 +02:00
parent f328915b1d
commit da54504781
53 changed files with 1276 additions and 0 deletions

2
.gitattributes vendored Normal file
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*.npy filter=lfs diff=lfs merge=lfs -text
*.dat filter=lfs diff=lfs merge=lfs -text

3
.gitignore vendored
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# phy
.phy/
# ---> Python # ---> Python
# Byte-compiled / optimized / DLL files # Byte-compiled / optimized / DLL files
__pycache__/ __pycache__/

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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

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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

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expipe.yaml Executable file
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{database_version: 2, project: septum-mec, type: project}

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probes/tetrode_16.prb Normal file
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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],
},
}

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probes/tetrode_32.prb Normal file
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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],
}
}

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scripts/backup_action Executable file
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#!/bin/bash
rsync -rzuP --exclude=.phy actions/$1 nird:/projects/NS9048K/NORSTORE_OSL_DISK/NS9048K/server/septum-mec/actions

2
scripts/fetch_action Executable file
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#!/bin/bash
rsync -rzv --progress nird:/projects/NS9048K/NORSTORE_OSL_DISK/NS9048K/server/septum-mec/actions/$1 actions

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scripts/fetch_action_not_yaml Executable file
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#!/bin/bash
rsync -rzv --progress --exclude="*.yaml" nird:/projects/NS9048K/NORSTORE_OSL_DISK/NS9048K/server/septum-mec/actions/$1 actions

2
scripts/fetch_elphys Executable file
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#!/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

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scripts/git_push_batch Executable file
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#!/bin/bash
for ((n=$1;n>0;n-=1))
do
git push origin HEAD~$n:master
done
git push

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scripts/phy2exdir_all_actions Executable file
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#!/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

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scripts/push_processing Executable file
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#!/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

5
scripts/reset_from_nird Executable file
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#!/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

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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

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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

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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

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templates/analgesia.yaml Normal file
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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

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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.

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templates/behavior.yaml Normal file
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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.

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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

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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.

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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.

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registered: '2018-10-25T21:55:28'
identifier: environment_surgery_station
name: environment_surgery_station
todo: todo

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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

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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: ''

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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: ''

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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

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registered: '2018-10-25T21:55:28'
identifier: hardware_blue_laser
name: hardware_blue_laser
todo: todo

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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

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TODO: TODO
registered: '2018-10-25T21:55:28'
identifier: hardware_laser_device
name: hardware_laser_device

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TODO: TODO
registered: '2018-10-25T21:55:28'
identifier: hardware_laser_measure_device
name: hardware_laser_measure_device

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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: ''

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registered: '2018-10-25T21:55:28'
identifier: hardware_microdrive_optetrode
name: hardware_microdrive_optetrode
todo: todo

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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

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registered: '2018-10-25T21:55:28'
identifier: hardware_openephys_optogenetics
name: hardware_openephys_optogenetics

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registered: '2018-10-25T21:55:28'
identifier: hardware_optic_fibre
name: hardware_optic_fibre
todo: todo

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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: ''

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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

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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

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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.

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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.

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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.

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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

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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.

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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.

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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.

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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

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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 .

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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 .

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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.

46
templates/subject.yaml Normal file
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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