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adamltyson committed May 23, 2024
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Expand Up @@ -31,7 +31,7 @@ Support for customising data structure (e.g. specific mandatory elements or new

**Q4 2025**

Export of NeuroBlueprint projects to [Neurodata Without Borders](https://www.nwb.org/) format.
Export of NeuroBlueprint projects to [Neurodata Without Borders](https://www.nwb.org/) format

(behaviour)=
## Behavioural analysis
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**Q4 2024**

- Implement [inter-session alignment methods](https://github.com/SpikeInterface/spikeinterface/issues/2626) in SpikeInterface.
- Implement [inter-session alignment methods](https://github.com/SpikeInterface/spikeinterface/issues/2626) in SpikeInterface

**Q2 2025**

Expand All @@ -82,22 +82,23 @@ and [standardise](https://github.com/SpikeInterface/spikeinterface/issues/2303)
**Current status**

Our computational anatomy work is based around the [BrainGlobe Initiative](https://brainglobe.info). BrainGlobe is
centered around the [BrainGlobe Atlas API](https://brainglobe.info/documentation/brainglobe-atlasapi/index.html) which
centered on the [BrainGlobe Atlas API](https://brainglobe.info/documentation/brainglobe-atlasapi/index.html) which
provides a common interface to multiple anatomical atlases. Currently, there are tools for:
- 3D whole brain microscopy registration ([brainreg](https://brainglobe.info/documentation/brainreg/index.html))
- 3D cell detection in large images ([cellfinder](https://brainglobe.info/documentation/cellfinder/index.html))
- Analysis of arbitrary shaped structures in atlas space such as lesions and implanted devices
([brainglobe-segmentation](https://brainglobe.info/documentation/brainglobe-segmentation/index.html))
- Visualisation of atlas registered data ([brainrender](https://brainglobe.info/documentation/brainrender/index.html) &
- Visualisation of atlas registered data ([brainrender](https://brainglobe.info/documentation/brainrender/index.html),
[brainrender-napari](https://github.com/brainglobe/brainrender-napari) &
[brainglobe-heatmap](https://brainglobe.info/documentation/brainglobe-heatmap/index.html))
- Various small tasks such as [reorienting anatomical images](https://brainglobe.info/documentation/brainglobe-space/index.html)

**Future**

BrainGlobe is a large project with many short- and long-term aims. Our two main goals are to:
- Allow for all neuroscience histology analysis and visualisation tasks to be carried out easily in a single
environment. This includes 2D & 3D data in all common animal models
- Create an end-to-end pipeline to analyse mouse brains imaged with a [mesoSPIM](https://mesospim.org/)
environment. This includes 2D & 3D data in all common animal models.
- Create an end-to-end pipeline to analyse mouse brains imaged with a [mesoSPIM](https://mesospim.org/).

For full details, please see the [BrainGlobe roadmap](https://brainglobe.info/community/roadmaps/index.html).

Expand All @@ -111,15 +112,15 @@ data analysis (e.g. [pynapple](https://pynapple-org.github.io/pynapple/)) and so
**Q3 2024**

- Export of behavioural timeseries from `movement` in [Neurodata Without Borders](https://www.nwb.org/) format, so it can
be loaded into [pynapple](https://pynapple-org.github.io/pynapple/).
be loaded into [pynapple](https://pynapple-org.github.io/pynapple/)

**Q2 2025**

- Export of spike times from `spikewrap` in [Neurodata Without Borders](https://www.nwb.org/) format, so it can
be loaded into [pynapple](https://pynapple-org.github.io/pynapple/).
be loaded into [pynapple](https://pynapple-org.github.io/pynapple/)

- Integration of `spikewrap` and `brainglobe-segmentation` to use the anatomical location of probe recordings as part of
the analysis.
the analysis

## Teaching
**Current status**
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