[ENH] microelectrode electrophysiology specification (BEP032) #1705

yarikoptic · 2024-02-14T15:24:13Z

Replaces #1352 submitted from a fork outside of bids-specification.

Add specification for microelectrode electrohpysiology datasets based on the BEP032 proposal

Note

We meet regularly and everyone is welcome

Next meeting: insert date on URL to join

Communication channel: https://framalistes.org/sympa/info/neuroscience-data-structure

Tip

HTML preview of this BEP

To use this WiP schema on sample datasets, see https://deno.land/x/[email protected]#modifying-and-building-a-new-schema on how to use "stock" bids-validator with a custom schema. (attn @TheChymera)

TODOs

Issues this PR would likely to address

Fixes run node tests in github actions legacy-validator#1375

Issues to see being addressed while working on this BEP (likely to move above) or not (moved below):

Other issues which relate but not in scope here and provided for reference/backreference

… _acq-

src/schema/rules/files/raw/channels.yaml

TheChymera · 2024-03-06T16:39:46Z

src/schema/objects/columns.yaml

@@ -42,6 +42,38 @@ age:
    for privacy purposes.
  type: number
  unit: year
+alpha_rotation:


I'd really recommend renaming the rotation axes to yaw, roll, and pitch (that would be the analogous angle order). There was no consensus either way on the google docs discussion. Someone said both are confusing, which I guess might be expected, but alpha, beta, gamma, are just more confusing...

I agree -- very adhoc. Let's discuss in google doc

https://docs.google.com/document/d/1oG-C8T-dWPqfVzL2W8HO3elWK8NIh2cOCPssRGv23n0/edit?disco=AAAA4fkI4eY

Could you chime in? I think the other guy commenting might be amenable to accepting this as well.

I agree that both are confusing, but at least alpha, beta and gamma are SO confusing that everyone realizes that additional specification is needed to define them properly. With roll, yaw and pitch it seems at first that all is clear, until you have a number of different people go through different use cases. See the more challenging examples that I posted on the google doc under https://docs.google.com/document/d/1oG-C8T-dWPqfVzL2W8HO3elWK8NIh2cOCPssRGv23n0/edit?disco=AAAA4fkI4eY

@robertoostenveld sorry, I only now saw the update, reply there. I don't think confusion on purpose is good in this case, because the documentation is very eclectic so we might be sending people down rabbit holes. Wiki, where people will invariably go first, does a particularly poor job explaining both euler and TB angles for the casual non-mathematics-versed user. The only thing that wiki has going for it here are the aircraft animations on the TB page. Yaw, Pitch, Roll, will be intuited correctly as long as we specify the starting postion. That we can do (1) as (I think, it's pretty vague) is currently proposed, aligning the implant with the world coordinate system (meaning most implants will be at yaw 0 pitch -90 roll 0) or (2) relative to the implantation stereotax normal (meaning most implants will be at 0 0 0).

For comparison, Euler commonly has the normal pointing up so most implants will be.... 0 -180 0 🤔

in the last BEP032 meeting we discussed further and wanted to follow this approach now (based on the Allen Inst. standard and IBL standard):

Assumption: x,y,z is posterior, ventral, right (unit needs to be specified).

Translational origin (0,0,0) needs to be defined (typically Bregma for rodents).

Rotational origin (0,0,0) is the probe facing up with the tip facing forward. Rotations are all clockwise in degrees and around the tip. For multi-shank probes, the “tip” of the probe is defined as the end of the left shank if you are looking at the electrodes.

yaw: clockwise when looking down

pitch: In the direction of the electrode face

roll: clockwise when looking down at the probe

The depth (unit needs to be specified) is a translation in the direction that the tip is pointing.

We need to add a “probe_model”, which references probeinterface_library

versioning of probe library files (raised here)

annotation of “tip” position (raised here)

NOTE: We need to change the electrode x,y,z.
X,y,z in BIDS refers to location in brain, not on probe.

TheChymera · 2024-03-06T16:46:27Z

src/schema/objects/columns.yaml

@@ -391,6 +462,12 @@ reference__ieeg:
    - type: string
      enum:
        - n/a
+reference_atlas:


The “reference atlas” if you visually verify the area is basically the atlas you looked at before you nod and said “eh, good enough”. This seems at once an overly detailed (does this really matter? the coordinates are commonly given with sub-mm precision) and underdetermined (what coordinates did you look at in the atlas?). I think it's best just to drop this.

TheChymera · 2024-03-12T01:33:27Z

Also relevant if you'd like to comment. → https://docs.google.com/document/d/1oG-C8T-dWPqfVzL2W8HO3elWK8NIh2cOCPssRGv23n0/edit?disco=AAABIzHGpUU

TheChymera · 2024-03-12T01:57:39Z

Also I forgot to link to this when I wrote it → https://docs.google.com/document/d/1oG-C8T-dWPqfVzL2W8HO3elWK8NIh2cOCPssRGv23n0/edit?disco=AAABIGPAMOw

src/schema/rules/files/raw/ephys.yaml

…t was missing

src/schema/objects/datatypes.yaml

src/schema/objects/modalities.yaml

src/schema/objects/suffixes.yaml

src/modality-specific-files/microelectrode-electrophysiology.md

…ctrode Electrophysiology

src/modality-specific-files/microelectrode-electrophysiology.md

* test * MACROS___make_suffix_table * markdown * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * undoing changes to yaml files * adding chanell * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update src/modality-specific-files/microelectrode-electrophysiology.md Co-authored-by: Yaroslav Halchenko <[email protected]> * Update src/modality-specific-files/microelectrode-electrophysiology.md Co-authored-by: Yaroslav Halchenko <[email protected]> * Update src/modality-specific-files/microelectrode-electrophysiology.md Co-authored-by: Yaroslav Halchenko <[email protected]> * Update src/modality-specific-files/microelectrode-electrophysiology.md Co-authored-by: Yaroslav Halchenko <[email protected]> * Update src/modality-specific-files/microelectrode-electrophysiology.md Co-authored-by: Yaroslav Halchenko <[email protected]> * Update src/modality-specific-files/microelectrode-electrophysiology.md Co-authored-by: Yaroslav Halchenko <[email protected]> * Update src/modality-specific-files/microelectrode-electrophysiology.md Co-authored-by: Yaroslav Halchenko <[email protected]> * adding General ephys metadata * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Examples of real datasets * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Minor tuneups to formatting --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Yaroslav Halchenko <[email protected]>

* [FIX] Minor YAML formatting * [ENH] Added additional birthdate column for participants.tsv * [ENH] Added age_category, age_type and corresponding enums * [ENH] Added surgery_date column * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Reverted changes that better suit in a PR against master * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [ENH] Added tabular_data file and columns for _probes.tsv * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [ENH] Added tabular_data rules and columns for _electrodes.tsv * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [ENH] Added tabular_data rules for _electrodes.tsv * [ENH] Added tabular_data rules and columns for _channels.tsv * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [FIX] Fixed pre-commit errors * [ENH] Added additional ephys columns for events.tsv * [ENH] Added tabular data rules for events.tsv to include ephys related columns * [ENH] Added metadata entities for ephys setup metadata * [ENH] Created sidecar rule file for ephys metadata and added data origin and setup fields * Made schema changes to match microephys data type * Renamed rule files from ephys to microephys * Made schema changes to match microephys data type * [ENH] Added objects and rules for coordinate system sidecar file * [ENH] Added processing microephys metadata field in rules * [ENH] Added pharmaceuticals microephys metadata field in rules * [ENH] Added supplementary microephys metadata field and rules * [ENH] Added sample microephys metadata rules * [ENH] Added task microephys metadata rules * Fixed example language convention * Added microephys in schema rule modality * Corrected SampleThickness to SliceThickness * Add yaml document separator for microephys rules file It is optional, and adding does not solve anything but makes it consistent with the other files in the folder * BF: should be a dict, not a list of dicts --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Yaroslav Halchenko <[email protected]>

bendichter · 2024-11-20T15:18:06Z

src/schema/rules/tabular_data/microephys.yaml

+    alpha_rotation: recommended
+    beta_rotation: recommended
+    gamma_rotation: recommended


todo: switch out for yaw, pitch and roll

* origin/master: (288 commits) chore(deps): bump codecov/codecov-action from 4 to 5 (#1989) chore: Bump schema post-dev version schema-0.11.3.post3 chore(ci): Fix pytest call for make_archive chore: Remove excess test data from bidsschematools installation directories (#1985) feat(cli): Add tool for filename validation for use in pre-receive hooks (#1986) rm COC (#1979) chore: Bump schema post-dev version schema-0.11.3.post2 Update CONTRIBUTING.md (#1978) fix(schema): Check SliceTiming length against SliceEncodingDirection fix(schema): Do not warn about missing events for task-noise fix(schema): Check for existence of stim_files in beh.tsv chore: Use GITHUB_REF(_NAME) correctly chore: Debug environment chore: Bump schema post-dev version schema-0.11.3.post1 chore: Output version, set correct env var chore: Update publish_schema to publish post-releases fix(schema): Include changes to schema that do not modify spec ... Conflicts: mkdocs.yml src/schema/objects/columns.yaml src/schema/objects/metadata.yaml src/schema/objects/modalities.yaml src/schema/objects/suffixes.yaml src/schema/rules/modalities.yaml

yarikoptic · 2024-11-20T16:01:15Z

src/modality-specific-files/microelectrode-electrophysiology.md

+
+
+```
+samples.tsv


use MACROS___make_filetree_example

src/modality-specific-files/microelectrode-electrophysiology.md

* origin/master: (26 commits) Update tools/schemacode/src/bidsschematools/types/namespace.py fail build on macro fails graceful error when failing to load invalid yml fix Update mkdocs.yml fix more seg Update src/modality-specific-files/electroencephalography.md fix channel, elec, sim recording fix key value and in-out fix tabular and seg reset fix internal links enh: Link all DICOM tags following standard pattern chore(links): Fix http -> https 301 redirects Update Release_Protocol.md (#1997) schema-1.0.1-dev schema-1.0.0 [SCHEMA] Allow physio files for anat datatype (#1961) FIX: Add 1.10.0 to known versions list (#1994) ...

…tion

src/schema/objects/columns.yaml

src/schema/rules/tabular_data/microephys.yaml

bendichter · 2024-12-18T15:14:05Z

src/schema/objects/entities.yaml

@@ -342,12 +342,12 @@ split:
  display_name: Split
  description: |
    In the case of long data recordings that exceed a file size of 2Gb,
-    `.fif` files are conventionally split into multiple parts.
-    Each of these files has an internal pointer to the next file.
+    `.fif`, `.nwb`, `.nix` files are conventionally split into multiple parts.


NWB files that exceed 2GB are not "conventionally" split into multiple parts. I don't know if this is true for NIX but I doubt it

we should look into https://bids-specification.readthedocs.io/en/stable/appendices/entities.html#split may be it would apply

Co-authored-by: Peyman Najafi <[email protected]>

bendichter · 2024-12-18T15:25:16Z

src/schema/rules/tabular_data/microephys.yaml

+    alpha_rotation: recommended
+    beta_rotation: recommended
+    gamma_rotation: recommended


Suggested change

alpha_rotation: recommended

beta_rotation: recommended

gamma_rotation: recommended

yaw: recommended

pitch: recommended

roll: recommended

* cutting line lenghts * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * marking json examples * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * microephysChannels --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

bendichter · 2024-12-18T15:27:07Z

src/modality-specific-files/microelectrode-electrophysiology.md

+probe_id	hemisphere	x	y	z	type		material	location
+p023		left		-11.87	-1.30	-3.37	utah-array	iridium-oxide	V1
+p023		left		-11.64	0.51	-4.20	utah-array	iridium-oxide	V2
+p021		left		-12.11	-3.12	-2.54	utah-array	iridium-oxide	V4
+p021		left		-9.94	-1.19	-2.86	utah-array	iridium-oxide	V3


Suggested change

probe_id hemisphere x y z type material location

p023 left -11.87 -1.30 -3.37 utah-array iridium-oxide V1

p023 left -11.64 0.51 -4.20 utah-array iridium-oxide V2

p021 left -12.11 -3.12 -2.54 utah-array iridium-oxide V4

p021 left -9.94 -1.19 -2.86 utah-array iridium-oxide V3

probe_id hemisphere x y z type material location

p023 left -11.87 -1.30 -3.37 utah-array iridium-oxide V1

p023 left -11.64 0.51 -4.20 utah-array iridium-oxide V2

p021 left -12.11 -3.12 -2.54 utah-array iridium-oxide V4

p021 left -9.94 -1.19 -2.86 utah-array iridium-oxide V3

bendichter · 2024-12-18T15:29:01Z

src/modality-specific-files/microelectrode-electrophysiology.md

+```
+dataset_description.json
+tasks.tsv
+tasks.json
+participants.tsv
+sub-A/
+  	ses-20220101/
+    		ephys/
+        sub-A_ses-20220101_task-nosepoke_ephys.nix
+        sub-A_ses-20220101_task-nosepoke_ephys.json
+        sub-A_ses-20220101_task-nosepoke_events.tsv
+        sub-A_ses-20220101_task-rest_ephys.nix
+        sub-A_ses-20220101_task-rest_ephys.json
+        sub-A_ses-20220101_channels.tsv
+        sub-A_ses-20220101_electrodes.tsv
+        sub-A_ses-20220101_probes.tsv
+  	ses-20220102/
+    		ephys/
+        sub-A_ses-20220102_task-rest_ephys.nix
+        sub-A_ses-20220102_task-rest_ephys.json
+        sub-A_ses-20220102_channels.tsv
+        sub-A_ses-20220102_electrodes.tsv
+        sub-A_ses-20220102_probes.tsv
+```


to do: use filetree macro

bendichter · 2024-12-18T15:37:33Z

src/schema/objects/columns.yaml

+  name: alpha_rotation
+  display_name: Alpha rotation
+  description: |
+    Euler angle to match probe extension dimensions (width, height, depth) to global x, y, z coordinates.


Suggested change

name: alpha_rotation

display_name: Alpha rotation

description: |

Euler angle to match probe extension dimensions (width, height, depth) to global x, y, z coordinates.

name: roll

display_name: Roll rotation

description: |

Clockwise rotation when looking down at the probe.

bendichter · 2024-12-18T15:37:43Z

src/schema/objects/columns.yaml

@@ -45,6 +45,40 @@ age:
    "Description": "Subject age in postnatal years",
    "Units": "year",
  }
+alpha_rotation:


Suggested change

alpha_rotation:

roll:

bendichter · 2024-12-18T15:38:46Z

src/schema/objects/columns.yaml

+beta_rotation:
+  name: beta_rotation
+  display_name: Beta rotation
+  description: |
+    Euler angle to match probe extension dimensions (width, height, depth) to global x, y, z coordinates.


Suggested change

beta_rotation:

name: beta_rotation

display_name: Beta rotation

description: |

Euler angle to match probe extension dimensions (width, height, depth) to global x, y, z coordinates.

pitch:

name: pitch

display_name: Pitch rotation

description: Rotation in the direction of the electrode face, in degrees.

bendichter · 2024-12-18T15:40:09Z

src/schema/objects/columns.yaml

+gamma_rotation:
+  name: gamma_rotation
+  display_name: Gamma rotation
+  description: |
+    Euler angle to match probe extension dimensions (width, height, depth) to global x, y, z coordinates.


Suggested change

gamma_rotation:

name: gamma_rotation

display_name: Gamma rotation

description: |

Euler angle to match probe extension dimensions (width, height, depth) to global x, y, z coordinates.

yaw:

name: yaw

display_name: Yaw rotation

description: Rotation clockwise when looking down.

bendichter · 2024-12-18T15:41:12Z

src/schema/objects/columns.yaml

+height__probes:
+  name: height
+  display_name: Height
+  description: |
+    Physical height of the probe, for example, '5'.
+    This dimension corresponds to the y’axis of the Euler transformation defined by
+    alpha, beta and gamma rotations values below.
+  type: number


Suggested change

height__probes:

name: height

display_name: Height

description: |

Physical height of the probe, for example, '5'.

This dimension corresponds to the y’axis of the Euler transformation defined by

alpha, beta and gamma rotations values below.

type: number

I don't understand what this is supposed to be

bendichter · 2024-12-18T15:41:37Z

src/schema/objects/columns.yaml

+width__probes:
+  name: width
+  display_name: Width
+  description: |
+    Physical width of the probe, for example, '5'.
+    This dimension corresponds to the x’axis of the Euler transformation defined by
+    alpha, beta and gamma rotations values.
+  type: number


Suggested change

width__probes:

name: width

display_name: Width

description: |

Physical width of the probe, for example, '5'.

This dimension corresponds to the x’axis of the Euler transformation defined by

alpha, beta and gamma rotations values.

type: number

I don't understand what this is supposed to be.

Add first BEP032 objects

7ec5d5e

yarikoptic requested review from tsalo and erdalkaraca as code owners February 14, 2024 15:24

yarikoptic mentioned this pull request Feb 14, 2024

[ENH] Add BEP032 (microelectrode electrophysiology) specification #1352

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Allow for using an arbitrary suffix and/or arbitrary entity bids-standard/bids-2-devel#63

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Add _acq- to ephys, add _channels and _coords

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Fix preferably typo

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[SCHEMA] Remove stale test comment -- test no longer fails! #1727

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Draft examples for BEP032 on animal electrophysiology bids-standard/bids-examples#430

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Automatic generation of extra-fields template forms from yaml-based schema (BIDS standard) elabftw/elabftw#5023

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TheChymera force-pushed the bep032 branch from cde80a6 to e2030ac Compare April 17, 2024 21:26

Added probes file

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Remi-Gau changed the title ~~[ENH] Add BEP032 (microelectrode electrophysiology) specification~~ [ENH] microelectrode electrophysiology specification (BEP032) Apr 18, 2024

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src/modality-specific-files/microelectrode-electrophysiology.md

```

samples.tsv

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use MACROS___make_filetree_example

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BEP032 support SpikeInterface/probeinterface#309

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Few fixes to the schema from review

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Co-authored-by: Peyman Najafi <[email protected]>

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Formalize specification of shape(s) (AKA contour(s)) #2013

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