diff --git a/src/modality-specific-files/microelectrode-electrophysiology.md b/src/modality-specific-files/microelectrode-electrophysiology.md index 39b5098cc7..f056ad0067 100644 --- a/src/modality-specific-files/microelectrode-electrophysiology.md +++ b/src/modality-specific-files/microelectrode-electrophysiology.md @@ -30,12 +30,12 @@ The current list of allowed data file formats: | [Neuroscience Information Exchange Format](https://nixio.readthedocs.io/en/latest/) | `.nix` | A generic and open framework with an hdf5 backend and a defined interface to many ephys formats via the [Neo library](https://neo.readthedocs.io/en/latest/). The `.nix` file has to contain a valid Neo structure. | | [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 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)). +Both of these formats can also store essential metadata of the datasets. +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)). ## @@ -88,11 +88,11 @@ 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**, and the listed required fields below must be included if a `*_coordsystem.json` file is provided. +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). +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: @@ -109,37 +109,37 @@ 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, or rendering of the electrodes on the brain. +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). +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. +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 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. +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. +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-