diff --git a/docs/modules/image/multi_channel_image.md b/docs/modules/image/multi_channel_image.md new file mode 100644 index 0000000..7521a2e --- /dev/null +++ b/docs/modules/image/multi_channel_image.md @@ -0,0 +1,14 @@ +## MultiChannelImage class +This class makes our code a bit more standardized on how multi-channel images are handled internally. +We use Xarray for the representation of the data and basically provide a wrapper around it providing reusable blocks of common functionality. + +The basic convention is to use the dimensions $(c, y, x)$ for the channel, $y$ and $x$ dimensions, respectively. +The channels have coordinates in the DataArray, describing the channel names. + +### Flat representation + +TODO To be described, since it is a bit tricky with the whole multi-index support. + +### API Reference + +... depiction.image. diff --git a/docs/modules/persistence/.pages b/docs/modules/persistence/.pages new file mode 100644 index 0000000..7aaa7ae --- /dev/null +++ b/docs/modules/persistence/.pages @@ -0,0 +1,4 @@ +nav: + - general_overview.md + - msi_data.md + - ... diff --git a/docs/modules/persistence.md b/docs/modules/persistence/general_overview.md similarity index 100% rename from docs/modules/persistence.md rename to docs/modules/persistence/general_overview.md diff --git a/docs/modules/persistence/image_data.md b/docs/modules/persistence/image_data.md new file mode 100644 index 0000000..b167178 --- /dev/null +++ b/docs/modules/persistence/image_data.md @@ -0,0 +1,4 @@ +# Image data +## Format: OME-TIFF + +## Format: NetCDF4 diff --git a/docs/modules/persistence/msi_data.md b/docs/modules/persistence/msi_data.md new file mode 100644 index 0000000..8e11526 --- /dev/null +++ b/docs/modules/persistence/msi_data.md @@ -0,0 +1 @@ +# MSI Data diff --git a/mkdocs.yml b/mkdocs.yml index 33b66df..5ca00a6 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -36,3 +36,4 @@ plugins: show_symbol_type_heading: yes show_source: no members_order: alphabetical + - awesome-pages diff --git a/pyproject.toml b/pyproject.toml index 4227605..e81c6d1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -84,6 +84,7 @@ doc = [ "mkdocs", "mkdocs-material", "mkdocstrings[python]", + "mkdocs-awesome-pages-plugin", ] apps = [ "bfabric @ git+https://github.com/fgcz/bfabricPy.git@main"