Merge pull request #96 from brainglobe/roadmap

Add the November 2023 roadmap

docs/source/community/index.md

@@ -3,6 +3,7 @@
 ```{toctree}
 :maxdepth: 1
 developers/index
+roadmaps/index
 releases/index
 external-tools
 Sample datasets <https://gin.g-node.org/BrainGlobe>

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
+```

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))