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adamltyson merged 2 commits into from
Dec 1, 2025
Merged

Standardise track descriptions #204

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2bbc897
Rename instructors sections
Dec 1, 2025
0e5beee
Standardise track formatting
Dec 1, 2025
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11 changes: 5 additions & 6 deletions docs/source/open-software-summer-school/2026/animals-in-motion.md
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Expand Up @@ -28,9 +28,8 @@ While icons of mice are used for illustration, the course content should be appl

```

### Core workshop

We will cover the following topics from **Monday to Wednesday**:
### Core workshop (Monday - Wednesday)
We will cover the following topics during the first three days:

* **Introduction:** a big-picture overview of analysis workflows and tools for animal behaviour.
* **Deep learning for computer vision:** a primer on the key concepts and technologies that underpin most markerless tracking approaches.
Expand All @@ -39,9 +38,9 @@ We will cover the following topics from **Monday to Wednesday**:
* **Behaviour segmentation:** a primer on decomposing continuous motion into discrete behaviours, followed by a practical tutorial of a supervised behaviour segmentation tool.


### Collaboration days
### Collaboration days (Thursday - Friday)

The final two days—**Thursday and Friday**—are dedicated to collaboration. We will join forces with participants from the **Large Array Data** track to work together on participant-led projects.
The final two days are dedicated to collaboration. We will join forces with participants from the **Large Array Data** track to work together on participant-led projects.

* **Skill building:** we'll start with a practical workshop on **Git and GitHub** to equip everyone with the necessary skills for collaborative coding.
* **Project-based work:** participants will self-organise into small teams to tackle projects hands-on. **Coding is not a requirement**; any idea that benefits from collaboration with other attendees is welcome. Potential project ideas include, but are not limited to:
Expand All @@ -62,7 +61,7 @@ Feel free to look through the handbook to get a sense of its contents, but keep

:::

## Instructors
## Confirmed Instructors
- [Niko Sirmpilatze](https://github.com/niksirbi)
- [Sofía Miñano](https://github.com/sfmig)
- [Chang Huan Lo](https://github.com/lochhh)
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11 changes: 5 additions & 6 deletions docs/source/open-software-summer-school/2026/brainglobe.md
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Expand Up @@ -16,9 +16,8 @@ It is aimed at those interested in learning about open-source tools for analysin

## Course overview

### Core workshop

We will cover the following topics from **Monday to Wednesday**:
### Core workshop (Monday - Wednesday)
We will cover the following topics during the first three days:

* **Introduction:** a high level overview of the BrainGlobe ecosystem of computational neuroanatomy tools, and what they enable.
* **Image analysis in `napari`:** basic concepts of image analysis using [`napari`](https://napari.org/stable/).
Expand All @@ -30,9 +29,9 @@ We will cover the following topics from **Monday to Wednesday**:
* Visualisation of data in atlas space with [`brainrender`](https://github.com/brainglobe/brainrender) and [`brainrender-napari`](https://github.com/brainglobe/brainrender-napari).
* **Programmatic access:** an introduction to interacting with the BrainGlobe ecosystem via scripting and the command line.

### Collaboration days
### Collaboration days (Thursday - Friday)

The final two days—**Thursday and Friday**—are dedicated to collaboration. We will join forces with participants from the **Extracellular Electrophysiology** track to work together on participant-led projects.
The final two days are dedicated to collaboration. We will join forces with participants from the **Extracellular Electrophysiology** track to work together on participant-led projects.

* **Skill building:** we'll start with a practical workshop on **Git and GitHub** to equip everyone with the necessary skills for collaborative coding.
* **Project-based work:** participants will self-organize into small teams to tackle projects hands-on. **Coding is not a requirement**; any idea that benefits from collaboration with other attendees is welcome. Potential project ideas include, but are not limited to:
Expand All @@ -43,7 +42,7 @@ The final two days—**Thursday and Friday**—are dedicated to collaboration. W
* *Prototype an idea:* test a cool new analysis idea or method on real-world data.
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@lochhh lochhh Dec 1, 2025

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these lines are repeated but inconsistently across

  • brainglobe.md
  • extracellular-electrophysiology.md
  • large-data.md
  • animals-in-motion.md

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@lochhh lochhh Dec 1, 2025

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I think the animals-in-motion one is the reviewed version, with "analyse" and "experiment with a new analysis or method"

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@adamltyson adamltyson Dec 1, 2025

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Cheers. I've raised #205

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@adamltyson adamltyson Dec 1, 2025

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I accidently pushed to main. @lochhh would you mind doing a post-hoc review to make sure I didn't make any silly mistakes (after advertising OSSS with the wrong year all morning!)?

* **Presentation:** you will have the opportunity to report your team's progress on the final afternoon.

## Instructors
## Confirmed Instructors
- [Alessandro Felder](https://github.com/alessandrofelder)
- [Igor Tatarnikov](https://github.com/IgorTatarnikov)
- [Adam Tyson](https://github.com/adamltyson)
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30 changes: 16 additions & 14 deletions docs/source/open-software-summer-school/2026/extracellular-electrophysiology.md
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Expand Up @@ -23,6 +23,8 @@ useful for those collecting large datasets and unsure how to process them.

## Course overview

### Core workshop (Monday - Wednesday)
We will cover the following topics during the first three days:
**Introduction**

We will begin with a high-level overview of extracellular electrophysiology data, including:
Expand Down Expand Up @@ -64,7 +66,20 @@ In the final session, we will focus on combining spike sorting outputs with beha
for analysis. This will include time alignment between electrophysiology and behavioural
events, and using [pynapple](https://github.com/pynapple-org/pynapple) to generate outputs (e.g. peristimulus time histograms).

## Instructors
### Collaboration days (Thursday - Friday)

The final two days are dedicated to collaboration. We will join forces with participants from the **BrainGlobe** track to work together on participant-led projects.

* **Skill building:** we'll start with a practical workshop on **Git and GitHub** to equip everyone with the necessary skills for collaborative coding.
* **Project-based work:** participants will self-organise into small teams to tackle projects hands-on. **Coding is not a requirement**; any idea that benefits from collaboration with other attendees is welcome. Potential project ideas include, but are not limited to:
* *Apply a tool:* use any learned software to analyse a new dataset (your own or a public one)
* *Give feedback:* report bugs and suggest features by raising issues on relevant open-source tools
* *Make a contribution:* submit a pull request to an open-source repository
* *Collaborative writing:* draft a white paper, blog post, or documentation together
* *Prototype an idea:* experiment with a new analysis or method
* **Presentation:** teams will have the opportunity to share their progress and outcomes on the final afternoon.

## Confirmed Instructors
* [Joseph Ziminski](https://github.com/JoeZiminski)
* [Chris Halcrow](https://github.com/chrishalcrow)

Expand All @@ -82,16 +97,3 @@ test dataset, so any fairly recent laptop will be sufficient. A GPU is not requi
### Data

Sample data will be provided, but if you have any of your own extracellular electrophysiology data, please bring it with you.

### Collaboration days

The final two days—**Thursday and Friday**—are dedicated to collaboration. We will join forces with participants from the **BrainGlobe** track to work together on participant-led projects.

* **Skill building:** we'll start with a practical workshop on **Git and GitHub** to equip everyone with the necessary skills for collaborative coding.
* **Project-based work:** participants will self-organise into small teams to tackle projects hands-on. **Coding is not a requirement**; any idea that benefits from collaboration with other attendees is welcome. Potential project ideas include, but are not limited to:
* *Apply a tool:* use any learned software to analyse a new dataset (your own or a public one)
* *Give feedback:* report bugs and suggest features by raising issues on relevant open-source tools
* *Make a contribution:* submit a pull request to an open-source repository
* *Collaborative writing:* draft a white paper, blog post, or documentation together
* *Prototype an idea:* experiment with a new analysis or method
* **Presentation:** teams will have the opportunity to share their progress and outcomes on the final afternoon.
6 changes: 3 additions & 3 deletions docs/source/open-software-summer-school/2026/large-data.md
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Expand Up @@ -17,9 +17,8 @@ This course is designed for researchers and students interested in learning abou


### Core workshop (Monday - Wednesday)


We will cover the following topics during the first three days:

* **Motivation:** we will show examples of large array datasets from neuroscience and imaging, discuss what research they enable, in what situations you should acquire them, and the computational challenges they pose.
* **Introduction to the [Zarr](https://zarr.dev/) and [Dask](https://www.dask.org/) libraries:** a short introduction to Python libraries that enable you to read, process, and write large array datasets.
* **Chunked, multi-scale file formats for large images:** a short introduction to the [OME-Zarr](https://ome-zarr-book.readthedocs.io/) format for large images and a practical tutorial to convert, process and visualise your large image data to OME-Zarr.
Expand All @@ -39,7 +38,8 @@ The final two days are dedicated to collaboration. We will join forces with part
* **Collaborative writing:** draft a white paper, blog post, or documentation together.
* **Prototype an idea:** test a cool new analysis or method on real-world data.
* **Presentation:** you will have the opportunity to report your team's progress on the final afternoon.
## Instructors

## Confirmed Instructors
- [Alessandro Felder](https://github.com/alessandrofelder)
- [Igor Tatarnikov](https://github.com/IgorTatarnikov)
- [David Stansby](https://github.com/dstansby)
Expand Down