diff --git a/README.md b/README.md
index 6af1a92..af27513 100644
--- a/README.md
+++ b/README.md
@@ -1,13 +1,13 @@
-# SWC-Blueprint
+# NeuroBlueprint
-![](docs/source/_static/swc-blueprint_logo-dark_no-text.png)
+![](docs/source/_static/NeuroBlueprint_logo-dark_no-text.png)
-`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.
+`NeuroBlueprint` 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.
+The [NeuroBlueprint 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.
+`NeuroBlueprint` 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.
+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/NeuroBlueprint/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.
-This repository hosts the source code for the [SWC-Blueprint website](https://swc-blueprint.neuroinformatics.dev).
+This repository hosts the source code for the [NeuroBlueprint website](https://neuroblueprint.neuroinformatics.dev).
diff --git a/docs/source/_static/swc-blueprint_logo-dark_no-text.png b/docs/source/_static/NeuroBlueprint_logo-dark_no-text.png
similarity index 100%
rename from docs/source/_static/swc-blueprint_logo-dark_no-text.png
rename to docs/source/_static/NeuroBlueprint_logo-dark_no-text.png
diff --git a/docs/source/_static/swc-blueprint_logo-light_no-text.png b/docs/source/_static/NeuroBlueprint_logo-light_no-text.png
similarity index 100%
rename from docs/source/_static/swc-blueprint_logo-light_no-text.png
rename to docs/source/_static/NeuroBlueprint_logo-light_no-text.png
diff --git a/docs/source/_static/swc-blueprint_project_tree_dark.png b/docs/source/_static/NeuroBlueprint_project_tree_dark.png
similarity index 100%
rename from docs/source/_static/swc-blueprint_project_tree_dark.png
rename to docs/source/_static/NeuroBlueprint_project_tree_dark.png
diff --git a/docs/source/_static/swc-blueprint_project_tree_light.png b/docs/source/_static/NeuroBlueprint_project_tree_light.png
similarity index 100%
rename from docs/source/_static/swc-blueprint_project_tree_light.png
rename to docs/source/_static/NeuroBlueprint_project_tree_light.png
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 9381d3d..fe89d09 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -17,7 +17,7 @@
# -- Project information -----------------------------------------------------
-project = 'SWC-Blueprint'
+project = 'NeuroBlueprint'
copyright = '2022, UCL'
author = 'Neuroinformatics Unit'
@@ -82,12 +82,12 @@
# a list of builtin themes.
#
html_theme = 'pydata_sphinx_theme'
-html_title = 'SWC-Blueprint'
+html_title = 'NeuroBlueprint'
# Redirect the webpage to another URL
# Sphinx will create the appropriate CNAME file in the build directory
# https://www.sphinx-doc.org/en/master/usage/extensions/githubpages.html
-html_baseurl = 'https://swc-blueprint.neuroinformatics.dev/'
+html_baseurl = 'https://neuroblueprint.neuroinformatics.dev/'
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
@@ -108,7 +108,7 @@
# Label for this link
"name": "GitHub",
# URL where the link will redirect
- "url": "https://github.com/neuroinformatics-unit/SWC-Blueprint", # required
+ "url": "https://github.com/neuroinformatics-unit/NeuroBlueprint", # required
# Icon class (if "type": "fontawesome"), or path to local image (if "type": "local")
"icon": "fa-brands fa-github",
# The type of image to be used (see below for details)
@@ -116,7 +116,7 @@
}
],
"logo": {
- "text": f"SWC-Blueprint v{release}",
+ "text": f"NeuroBlueprint v{release}",
"image_light": "logo_light.png",
"image_dark": "logo_dark.png",
},
diff --git a/docs/source/index.md b/docs/source/index.md
index 365a75d..7d10b8d 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -1,15 +1,15 @@
-# SWC-Blueprint
+# NeuroBlueprint
-
-
+
+
-**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.
+**NeuroBlueprint** 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.
+The [NeuroBlueprint 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.
+**NeuroBlueprint** 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.
+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/NeuroBlueprint/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.
```{toctree}
:maxdepth: 3
diff --git a/docs/source/specification.md b/docs/source/specification.md
index 32e50f7..218f994 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 **NeuroBlueprint** 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}
@@ -13,8 +13,8 @@ Standardised project folders contain data that are hierarchically structured acc
For example:
-
-
+
+
### Basic principles
@@ -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).
+**NeuroBlueprint** 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-