From 800ba580f05cc3b76c3390a8484b6d2d71e723da Mon Sep 17 00:00:00 2001 From: Peyman Najafi Date: Wed, 18 Dec 2024 16:26:07 +0100 Subject: [PATCH] Adopting the markdown line lengths for BEP032 (#2012) * 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> --- .../microelectrode-electrophysiology.md | 254 ++++++++++++++---- 1 file changed, 203 insertions(+), 51 deletions(-) diff --git a/src/modality-specific-files/microelectrode-electrophysiology.md b/src/modality-specific-files/microelectrode-electrophysiology.md index a12aadc2f6..68ce10fc9e 100644 --- a/src/modality-specific-files/microelectrode-electrophysiology.md +++ b/src/modality-specific-files/microelectrode-electrophysiology.md @@ -31,11 +31,12 @@ The current list of allowed data file formats: | [Neurodata Without Borders](https://www.nwb.org) | `.nwb` | An open data standard for neurophysiology, including data from intracellular and extracellular electrophysiology experiments. | Both of these formats can also store essential metadata of the datasets. -Some of these need to be duplicated in BIDS `.tsv` and `.json` sidecar files. -Even though the duplication requires additional effort to ensure the consistency of the data, it provides a number of advantages: -- Making the dataset easier for humans to scan as essential information is easily accessible without loading the data files -- The dataset follows the BIDS standard and can benefit from tools building on top of this standard, starting with [bids-validator](https://github.com/bids-standard/bids-validator). -- It simplifies the separation of data and basic metadata, for example to publish a dataset in a light-weight fashion with access to the data files on request (as implemented by [DataLad](https://www.datalad.org)). +Some of this metadata needs to be duplicated in BIDS `.tsv` and `.json` sidecar files. +Even though the duplication requires additional effort to ensure the consistency of the data, it provides several advantages: +- It makes the dataset easier for humans to scan, as essential information is easily accessible without loading the data files. +- The dataset adheres to the BIDS standard and can benefit from tools built on top of this standard, such as [bids-validator](https://github.com/bids-standard/bids-validator). +- It simplifies the separation of data and basic metadata, enabling, for example, the publication of a dataset in a lightweight fashion with access to the data files on request (as implemented by [DataLad](https://www.datalad.org)). + ## @@ -73,7 +74,6 @@ It follows the [general BIDS specifications to describe participants](../modalit On top of the existing columns that can be present in this file and that are described in the BIDS specifications (`participant_id`, `species`, `strain`, `strain_rrid`, `sex`, `handedness`, and `age`), we propose to allow adding the following ones: -{{ MACROS___make_columns_table("modality_agnostic.Participants_micro") }} # EPHYS specific files @@ -88,7 +88,12 @@ As with all tsv-based metadata files in BIDS the probes, electrodes and channels ## Coordinate System JSON (`*_coordsystem.json`) & Photos of electrode positions (`_photo.jpg`) -This file provides metadata on the global coordinate system in which the electrodes are placed. This file is RECOMMENDED, the listed required fields below have to be contained in case a `*_coordsystem.json` is provided. This system can be defined via reference pictures, anatomical landmarks, images of the brain or a reference atlas. For more details see the [BIDS Coordinate Systems specifications](../appendices/coordinate-systems.md). +This file provides metadata on the global coordinate system in which the electrodes are placed. +This file is **RECOMMENDED**, and the listed required fields below must be included if a `*_coordsystem.json` file is provided. + +The coordinate system can be defined using reference pictures, anatomical landmarks, brain images, or a reference atlas. +For more details, see the [BIDS Coordinate Systems specifications](../appendices/coordinate-systems.md). + Fields relating to the ephys probe and electrode positions: @@ -104,25 +109,38 @@ Fields relating to the ephys probe and electrode positions: ### Allowed 2D coordinate systems -If electrodes are localized in 2D space (only x and y are specified and z is `"n/a"`), then the positions in this file MUST correspond to the locations expressed in pixels on the photo/drawing/rendering of the electrodes on the brain. -In this case, `ephysCoordinateSystem` MUST be defined as `"Pixels"`, and `ephysCoordinateUnits` MUST be defined as `"pixels"` (note the difference in capitalization). -Furthermore, the coordinates MUST be (row,column) pairs, with (0,0) corresponding to the upper left pixel and (N,0) corresponding to the lower left pixel. +If electrodes are localized in 2D space (only `x` and `y` are specified, and `z` is `"n/a"`), +then the positions in this file MUST correspond to the locations expressed in pixels on the +photo, drawing, or rendering of the electrodes on the brain. + +In this case, `ephysCoordinateSystem` MUST be defined as `"Pixels"`, +and `ephysCoordinateUnits` MUST be defined as `"pixels"` (note the difference in capitalization). + +Furthermore, the coordinates MUST be `(row,column)` pairs, +with `(0,0)` corresponding to the upper-left pixel and `(N,0)` corresponding to the lower-left pixel. ### Photos of the electrode positions (`*_photo.jpg`) -These can include photos of the electrodes on the brain surface, photos of anatomical features or landmarks (such as sulcal structure), and fiducials. Photos can also include an X-ray picture, a flatbed scan of a schematic drawing made during surgery, or screenshots of a brain rendering with electrode positions. The photos may need to be cropped and/or blurred to conceal identifying features or entirely omitted prior to sharing, depending on obtained consent. +These can include photos of the electrodes on the brain surface, +photos of anatomical features or landmarks (such as sulcal structures), and fiducials. +Photos can also include an X-ray picture, a flatbed scan of a schematic drawing made during surgery, +or screenshots of a brain rendering with electrode positions. + +The photos may need to be cropped and/or blurred to conceal identifying features +or entirely omitted prior to sharing, depending on the obtained consent. If there are photos of the electrodes, the [`_acq-