diff --git a/docs/source/index.md b/docs/source/index.md index 55be05e..5792982 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -3,11 +3,11 @@ SWC-Blueprint logo SWC-Blueprint logo -`SWC-Blueprint` is a folder structure specification for (systems) neuroscience research projects. It is inspired by, and based on the [BIDS specification](https://bids-specification.readthedocs.io/en/stable/), widely used in human neuroimaging. +**SWC-Blueprint** is a folder structure specification for (systems) neuroscience research projects. It is inspired by, and based on the [BIDS specification](https://bids-specification.readthedocs.io/en/stable/), widely used in human neuroimaging. The [SWC-Blueprint specification](specification.md) provides a set of rules and guidelines for project folder organisation, ensuring consistent data management within and between labs. The focus is on ensuring minimal overhead for researchers. -`SWC-Blueprint` is being developed at the [Sainsbury Wellcome Centre (SWC) for Neural Circuits and Behaviour](https://www.sainsburywellcome.org/) by members of the [Neuroinformatics Unit (NIU)](https://neuroinformatics.dev/). As such, it prioritizes interoperability with NIU-developed data analysis tools. +**SWC-Blueprint** is being developed at the [Sainsbury Wellcome Centre (SWC) for Neural Circuits and Behaviour](https://www.sainsburywellcome.org/) by members of the [Neuroinformatics Unit (NIU)](https://neuroinformatics.dev/). As such, it prioritizes interoperability with NIU-developed data analysis tools. That said, the specification is designed to be as general as possible, and should be useful to anyone within the neuroscience field. We (the NIU) welcome [feedback](https://github.com/neuroinformatics-unit/SWC-Blueprint/discussions) and contributions from the wider community and commit to maintaining the specification as a living and evolving document. We will also collaborate with [ongoing efforts](https://github.com/INCF/neuroscience-data-structure) by the [INCF](https://www.incf.org/) and [BIDS community](https://bids.neuroimaging.io/) to extend the BIDS specification to non-human animal research. diff --git a/docs/source/specification.md b/docs/source/specification.md index 37fee27..8ea9f80 100644 --- a/docs/source/specification.md +++ b/docs/source/specification.md @@ -1,6 +1,6 @@ # The specification -The current version of `SWC-Blueprint` mainly aims to enforce a uniform and consistent [project folder structure](#project-folder-structure). +The current version of **SWC-Blueprint** mainly aims to enforce a uniform and consistent [project folder structure](#project-folder-structure). In addition, it also includes some non-mandatory conventions for [naming files](#file-naming-conventions) and storing [tabular metadata](#tabular-metadata). :::{note} @@ -26,13 +26,13 @@ For example: * `derivatives`: any processed data that is derived from `rawdata` (e.g. spike sorting or pose estimation). -* Data within the `rawdata` folder *must* be hierarchically structured into `subject/session/datatype` levels. Each level *must* contain at least one folder corresponding to the next (lower) level. +* Data within the `rawdata` folder *must* be hierarchically structured into subject/session/datatype levels. Each level *must* contain at least one folder corresponding to the next (lower) level. -* `subject` and `session` folder names *must* consist of key-value pairs separated by underscores, withous spaces e.g. `sub-001_id-5645332`. +* Subject and session folder names *must* consist of key-value pairs separated by underscores, without spaces e.g. `sub-001_id-5645332`. -* `datatype` folder names *must* be one of the following : `ephys`, `behav`, `funcimg`, `histology`. +* Datatype folder names *must* be one of the following : `ephys`, `behav`, `funcimg`, `histology`. -* If collected, `ephys`, `behav`, `funcimg` *must* be placed under the `session` level. If collected, `histology` *must* be placed under the `subject` level. +* If collected, `ephys`, `behav`, `funcimg` *must* be placed under the session level. If collected, `histology` *must* be placed under the subject level. Below we describe each level of the `rawdata` folder hierarchy in more detail. Though we impose no absolute requirements for the folder structure within `derivatives`, it *should* match the hierarchy in `rawdata` whenever possible. @@ -78,7 +78,7 @@ The following datatypes are supported: * `histology`: anatomical (e.g. serial-2-photon images) :::{note} -Unlike the first three `datatypes` that belong at the `session` level, `histology` belongs at the `subject` level. +Unlike the first three datatypes that belong at the session level, `histology` belongs at the subject level. ::: ### Example project folder @@ -110,7 +110,7 @@ A real project folder might look like: ## File naming conventions -`SWC-Blueprint` imposes no absolute requirements on file names. That said, below we provide some recommendations for file names, based on the [BIDS specification](https://bids-specification.readthedocs.io/en/stable/02-common-principles.html#filenames). +**SWC-Blueprint** imposes no absolute requirements on file names. That said, below we provide some recommendations for file names, based on the [BIDS specification](https://bids-specification.readthedocs.io/en/stable/02-common-principles.html#filenames). :::{admonition} What makes a good file name? :class: tip @@ -130,7 +130,7 @@ A real project folder might look like: * Anything after the left-most stop (`.`) is considered as the file extension. * `sub` and `ses` *should* be included in the filename. This can seem redundant, given that the file is already in a `sub-