# June 2024

One of our main goals in the team is to provide fully integrated, automated analysis tools for systems neuroscience 
data. As a researcher, this would mean providing only a set of configurations before running the analysis for an entire 
dataset, with results and quality metrics output for checking. This will avoid researchers needing to write 
custom preprocessing and analysis scripts that often duplicate existing efforts, and allows researchers to work 
together on community tools.

This is a long-term goal, and we are working across multiple themes towards achieving this. We are ensuring [data is 
organised in a standard way](data_management), a critical step towards automation. Currently, we are focused on 
building pipelines for [behaviour](behaviour), [electrophysiology](electrophysiology) and [anatomy](anatomy) that 
can ingest data from various acquisition systems into a common interface. These are critical steps towards the 
longer-term goal of multimodal integration. The detailed roadmap is split into these themes below.

(data_management)=
## Data management
**Current status**

We have developed [NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev/), a simple, standard data folder 
specification for (systems) neuroscience and [datashuttle](https://datashuttle.neuroinformatics.dev/), to automate the 
creation, validation and transfer of NeuroBlueprint projects. For more details on these specific projects, see the 
[NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev/roadmap.html) and 
[datashuttle](https://datashuttle.neuroinformatics.dev/pages/community/roadmap.html) roadmaps.

**Q4 2024**

Standardised metadata support

**Q2 2025**

Support for customising data structure (e.g. specific mandatory elements or new file types)

**Q4 2025**

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

(behaviour)=
## Behavioural analysis
**Current status**

We are building [movement](https://movement.neuroinformatics.dev/) a Python toolbox for analysis of animal tracking 
data. For more details on this specific project, see the [movement roadmap](https://movement.neuroinformatics.dev/community/roadmaps.html).

**Q3 2025**

- Support all common post pose-estimation analysis tasks
- Support for single experiments and complex multi-animal, multi-session datasets 
(by reading and writing to [NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev/) format)

**No current ETA**

- A common interface to prevalent pose estimation tools, and other machine-learning based object detection methods
- A common interface to methods for behavioural segmentation and classification

(electrophysiology)=
## Extracellular electrophysiology analysis
**Current status**

We are currently building [spikewrap](https://github.com/neuroinformatics-unit/spikewrap) (built on top of 
[SpikeInterface](https://spikeinterface.readthedocs.io/en/latest/)) for simple, routine analysis of extracellular 
electrophysiology analysis. For more details on this specific project, see the
[spikewrap roadmap](https://github.com/neuroinformatics-unit/spikewrap/issues/178).

**Q3 2024**

Contribute to ongoing SpikeInterface efforts to:
- [Improve documentation](https://github.com/SpikeInterface/spikeinterface/issues/2046)
- [Improve](https://github.com/SpikeInterface/spikeinterface/issues/2282) 
and [standardise](https://github.com/SpikeInterface/spikeinterface/issues/2303) the API

**Q4 2024**

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

**Q2 2025**

- Easy to use tool for all common extracellular electrophysiology analysis steps
- Support for single experiments and complex multi-animal, multi-session datasets
  (by reading and writing to [NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev/) format)

(anatomy)=
## Computational anatomy
**Current status**

Our computational anatomy work is based around the [BrainGlobe Initiative](https://brainglobe.info). BrainGlobe is
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),
  [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/).

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

## Multimodal integration
**Current status**

Currently, our data analysis tools are restricted to a single modality. It is important that multimodal data can be 
combined at the analysis stage e.g. to correlate neural activity and behaviour. There are some excellent existing packages for neurophysiological 
data analysis (e.g. [pynapple](https://pynapple-org.github.io/pynapple/)) and so we plan to leverage these.

**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/)

**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/)

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

## Teaching
**Current status**

Over the past 18 months, we have delivered a series of computational skills courses at the Sainsbury Wellcome Centre
(details can be found on the [Software Skills website](https://software-skills.neuroinformatics.dev/)).

**Q4 2025**

Over the next 18 months we will develop our existing courses into a coherent set of materials that can be used to 
deliver an introductory one-week course on the computational skills needed in systems neuroscience, including:
- Basic linux command line usage
- Version control
- Python programming
- Software development best practices
- Good data management
- High performance computing
- Video behavioural analysis
- Multiphoton image analysis
- Extracellular electrophysiology analysis
- Histology analysis