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BrainGlobe version 1 is here! Head over to the blog to find out more

May 2024#

The November 2023 roadmap was our first. This document looks back on the last six months of work and outlines plans for the next year.

Current status#

Progress since the last roadmap#

The past few months have focused mostly on improving the maintainability of BrainGlobe as a whole, and making it easier to develop new tools in the future. Some developments include (for more details on these, see the blog):

  • The brainreg napari plugin is now bundled with brainreg to simplify maintenance.

  • brainreg-segment is now called brainglobe-segmentation to reflect its future compatibility with other registration tools.

  • The old cellfinder command-line tool is now called brainmapper and is part of brainglobe-workflows. This is part of work to separate the core BrainGlobe software from convenience tools (“workflows”) developed for specific applications.

  • The old cellfinder-core and cellfinder-napari tools have been merged, and are now known just as cellfinder. This is to simplify maintenance and reduce confusion (we used to have three cellfinders!).

  • bg-space is now known as brainglobe-space to standardise naming.

  • bg-atlasapi and bg-atlasgen have been merged and are now known as brainglobe-atlasapi to standardise naming.

  • imio has been brought into the brainglobe-utils package, to reduce the number of packages we maintain.

  • We’ve increased the robustness of brainglobe-utils by adding lots of automated tests.

  • brainrender has been updated so that it now works with the newest versions of Python.

  • A new LineActor has been added to brainrender.

  • bgheatmap has been updated so that it now works with the newest versions of Python and now released as brainglobe-heatmap.

  • brainglobe version 1 has been released. This new “metapackage” allows one line installation of all BrainGlobe tools.

  • We’ve fixed a lot of small bugs and hugely reduced the number of open issues.

  • We’ve standardised the tooling for all repos to simplify development and maintenance.

  • We’ve released brainrender-napari to allow for visualisation of atlas-registered data in napari (alongside the existing brainrender).

  • We’ve fixed a number of scaling and rotation issues with some BrainGlobe atlases.

Issues#

  • It is not yet possible to carry out all BrainGlobe functionality via the GUI (although we are 90% of the way there)

  • Documentation for some tools is sparse

  • Docstrings are often missing, incomplete or not standardised

  • We have very few API docs

  • Test coverage is variable (some repos are in excellent shape, others not so much!)

  • cellfinder uses TensorFlow, and so we’re limited to what Python versions we can support for the metapackage

  • Only some tools are available on conda-forge, and so conda install brainglobe is not yet possible.

  • There’s still a lot of small bugs hanging around

  • Use of the napari plugins isn’t very integrated (lots of opening and closing, saving & reopening)

  • Some of the atlases have inconsistencies that make their use with particular tools difficult

Future#

Q3 2024#

  • PyTorch backend for cellfinder, enabling use with the latest versions of Python & release on conda-forge.

  • All tools installable via conda install brainglobe -c conda-forge

  • Automated benchmarks for cell detection on “real” (full size) data

  • Re-release of all (fully standardised) atlases

Q4 2024#

  • Generic layer interpreters (BrainGlobe/10)

  • All analyses possible without leaving napari

  • Automated benchmarks for 3D atlas registration on “real” (full size) data

  • Registration of 2D (e.g. conventional sections) data to an atlas

  • All tools fully documented

Q1 2025#

  • All visualisation possible without leaving napari

  • Consistent and documented API, e.g. from brainglobe import cellfinder or from brainglobe import cell_detector_3D (or both)

  • Registration of 3D subvolume data to an atlas

  • Intuitive navigation of napari plugins

    • Create “metaplugin”

Q2 2025#

  • Atlas generation within napari

  • Facilitate common analyses/visualisation within napari

    • Plot cells per brain region

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