diff --git a/docs/source/_static/NeuroBlueprint_logo-dark_no-text.png b/docs/source/_static/NeuroBlueprint_logo-dark_no-text.png old mode 100644 new mode 100755 index 449c9e3..ddc917b Binary files a/docs/source/_static/NeuroBlueprint_logo-dark_no-text.png and b/docs/source/_static/NeuroBlueprint_logo-dark_no-text.png differ diff --git a/docs/source/_static/NeuroBlueprint_logo-light_no-text.png b/docs/source/_static/NeuroBlueprint_logo-light_no-text.png old mode 100644 new mode 100755 index 66cd533..0d48013 Binary files a/docs/source/_static/NeuroBlueprint_logo-light_no-text.png and b/docs/source/_static/NeuroBlueprint_logo-light_no-text.png differ diff --git a/docs/source/_static/NeuroBlueprint_project_tree_dark.png b/docs/source/_static/NeuroBlueprint_project_tree_dark.png old mode 100644 new mode 100755 index 9f0145c..e1dc6a3 Binary files a/docs/source/_static/NeuroBlueprint_project_tree_dark.png and b/docs/source/_static/NeuroBlueprint_project_tree_dark.png differ diff --git a/docs/source/_static/NeuroBlueprint_project_tree_light.png b/docs/source/_static/NeuroBlueprint_project_tree_light.png old mode 100644 new mode 100755 index f5f400b..e63a81b Binary files a/docs/source/_static/NeuroBlueprint_project_tree_light.png and b/docs/source/_static/NeuroBlueprint_project_tree_light.png differ diff --git a/docs/source/specification.md b/docs/source/specification.md index 605b10f..323a023 100644 --- a/docs/source/specification.md +++ b/docs/source/specification.md @@ -30,9 +30,9 @@ For example: * 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`, `anat`. -* If collected, `ephys`, `behav`, `funcimg` *must* be placed under the session level. If collected, `histology` *must* be placed under the subject level. +* Datatype folders *must* be placed under the session 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. @@ -77,11 +77,8 @@ The following datatypes are supported: * `ephys`: electrophysiology (e.g. Neuropixel probes, tetrodes) * `behav`: behavioural (e.g. video and audio files, response logs) * `funcimg`: functional imaging (e.g. calcium and voltage imaging) -* `histology`: anatomical (e.g. serial-2-photon images) +* `anat`: anatomical (e.g. histology, using confocal or lightsheet) -:::{note} -Unlike the first three datatypes that belong at the session level, `histology` belongs at the subject level. -::: ### Example project folder A real project folder might look like: @@ -97,8 +94,9 @@ A real project folder might look like: │ │ └── behav/ │ │ ├── sub-001_ses-01_camera-01.wav │ │ └── sub-001_ses-01_data-responses.csv - │ └── histology/ - │ └── sub-001_image-brain.tiff + │ └── ses-02_date-20230311/ + │ └── anat/ + │ └── sub-001_image-brain.tiff └── derivatives/ └── sub-001_id-5645332/ ├── ses-01_date-20230310/ @@ -106,8 +104,9 @@ A real project folder might look like: │ │ └── sub-001_ses-01_data-spikes.npy │ └── behav/ │ └── sub-001_ses-01_data-poses.csv - └── histology/ - └── sub-001_ses-01_data-cellcounts.csv + └── ses-02_date-20230311/ + └── anat/ + └── sub-001_data-cellcounts.csv ``` ## File naming conventions