diff --git a/docs/source/community/index.md b/docs/source/community/index.md index 1339ebe3..4de0006d 100644 --- a/docs/source/community/index.md +++ b/docs/source/community/index.md @@ -3,6 +3,7 @@ ```{toctree} :maxdepth: 1 developers/index +roadmaps/index releases/index external-tools Sample datasets diff --git a/docs/source/community/roadmaps/index.md b/docs/source/community/roadmaps/index.md new file mode 100644 index 00000000..2468ffd7 --- /dev/null +++ b/docs/source/community/roadmaps/index.md @@ -0,0 +1,15 @@ +# Roadmaps + +BrainGlobe roadmaps give you an idea of where the project is heading over the next few months and years. +These roadmaps are usually at a high level for the BrainGlobe project as a whole. +Plans for individual tools are usually discussed on their respective repos, and +over at [Zulip](https://brainglobe.zulipchat.com/). + +BrainGlobe is a community project, and as such we welcome your feedback. Please [get in touch with us](/contact) if you have +any questions or suggestions. These roadmaps are living documents and will likely be revisited regularly. + +```{toctree} +:maxdepth: 1 + +november-2023 +``` \ No newline at end of file diff --git a/docs/source/community/roadmaps/november-2023.md b/docs/source/community/roadmaps/november-2023.md new file mode 100644 index 00000000..3dcc02b0 --- /dev/null +++ b/docs/source/community/roadmaps/november-2023.md @@ -0,0 +1,65 @@ +# November 2023 + +This roadmap reflects our current priorities which are to refactor and organise the BrainGlobe codebase. Many of these changes won't add any new features - they are largely aimed at making existing features more accessible (e.g. through a graphical user interface), ensure all tools are easier-to-install and at making BrainGlobe +easier to maintain and further develop in the long-term. We hope this will ensure that BrainGlobe is around for years to come, and that we have a solid platform to develop new tools and support a growing community in the future. + +## Current status +* BrainGlobe Atlas API provides a consistent interface to multiple anatomical atlases +* Separate tools for 3D cell detection ([`cellfinder-core`](https://github.com/brainglobe/cellfinder-core)), +3D atlas registration([`brainreg`](https://github.com/brainglobe/brainreg)), bulk segmentation +([`brainreg-segment`](https://github.com/brainglobe/brainreg-segment)) and 3D +visualisation ([`brainrender`](https://github.com/brainglobe/brainrender)) +* Plugins for 3D cell detection ([`cellfinder-napari`](https://github.com/brainglobe/cellfinder-napari)) and +registration ([`brainreg-napari`](https://github.com/brainglobe/brainreg-napari)) + +### Issues +* [`brainrender`](https://github.com/brainglobe/brainrender) has considerable technical debt +([brainrender/247](https://github.com/brainglobe/brainrender/issues/247)) +* Lots of repositories makes it more difficult to understand which tool does what, and to contribute +(e.g. [`cellfinder`](https://github.com/brainglobe/cellfinder), +[`cellfinder-core`](https://github.com/brainglobe/cellfinder-core), [`cellfinder-napari`](https://github.com/brainglobe/cellfinder-napari)) +* The mix of napari plugins, Python APIs and command line tools make the ecosystem appear more complicated than it should +* It is not yet possible to carry out all analyses and visualisation within a single platform (napari) + * Some non-image processing steps need to be carried out seperately (e.g. assigning cells to brain regions) + * Some visualisation relies on exporting data from napari to brainrender + +## v1 (Q4 2023) +* brainrender installable alongside analysis tools (cellfinder, brainreg, brainreg-segment) +* All tools installable via `pip install brainglobe` or `conda install brainglobe -c conda-forge` + +## v2 (Q2 2024) +* Consistent API, e.g. `from brainglobe import cellfinder` or `from brainglobe import cell_detector_3D` (or both) +* Carry out everything in v1 without leaving napari + * Atlas registration ([`brainreg-napari`](https://github.com/brainglobe/brainreg-napari)) + * Cell detection ([`cellfinder-napari`](https://github.com/brainglobe/cellfinder-napari)) + * Assign cells to brain regions (TBC) + * Analyse arbitrary ROIs ([`brainreg-segment`](https://github.com/brainglobe/brainreg-segment)) + * Visualisation ([`brainrender-napari`](https://github.com/brainglobe/brainrender-napari)) +* Automated benchmarks for analysis tools (cell detection & 3D atlas registration) on "real" (full size) data +* Combine napari plugins with backend to reduce number of repositories +([BrainGlobe/3](https://github.com/brainglobe/BrainGlobe/issues/3) & +([BrainGlobe/4](https://github.com/brainglobe/BrainGlobe/issues/4)) +* Remove existing `cellfinder` CLI to simplify naming ([BrainGlobe/6](https://github.com/brainglobe/BrainGlobe/issues/6)) +* Release [`brainglobe-workflows`](https://github.com/brainglobe/brainglobe-workflows), a collection of scripts to +facilitate common tasks (including replacing the `cellfinder` CLI) + +## v3 (Q4 2024) +* Intuitive navigation of napari plugins + * Create "metaplugin" +* Generic layer interpreters ([BrainGlobe/10](https://github.com/brainglobe/BrainGlobe/issues/10)) +* Refactored and documented Python API +* Facilitate common analyses/visualisation within napari + * Plot cells per brain region +* Sample data provided via napari + +## Other ongoing projects (release TBC) +* Arbitrary brain subvolume (2D or 3D) registration +([`brainglobe-registration`](https://github.com/brainglobe/brainglobe-registration)) +* Atlas generation tool (from raw data to BrainGlobe atlas), including +[`brainglobe-template-builder`](https://github.com/brainglobe/brainglobe-template-builder) +* More flexible BrainGlobe atlas API V2 ([bg-atlasapi/141](https://github.com/brainglobe/bg-atlasapi/issues/141)) +* New atlases + * Update Allen adult mouse brain atlas ([bg-atlasgen/46](https://github.com/brainglobe/bg-atlasgen/issues/46)) + * 3D Multimodal Developmental Mouse Brain atlases ([bg-atlasgen/71](https://github.com/brainglobe/bg-atlasgen/issues/71)) + * Human MRI atlases ([bg-atlasgen/85](https://github.com/brainglobe/bg-atlasgen/issues/85)) + * Update Waxholm rat atlas ([bg-atlasgen/84](https://github.com/brainglobe/bg-atlasgen/issues/84))