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Sep 26, 2024
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Updated behav course prerequisites #62

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Updated behav course prerequisites
niksirbi Sep 25, 2024
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niksirbi Sep 26, 2024
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5 changes: 4 additions & 1 deletion docs/source/courses/software-skills.md
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(general-software-skills)=
# General software skills for systems neuroscience

## Overview
Expand Down Expand Up @@ -62,7 +63,9 @@ Participants will get to train pose estimation models
with [SLEAP](https://sleap.ai/), analyse pose tracks
with [movement](https://movement.neuroinformatics.dev/), and extract behavioural syllables with [keypoint-moseq](https://keypoint-moseq.readthedocs.io/en/latest/index.html).

Full details can be found on the [course webpage](video-analysis).
:::{important}
Please install the necessary software and download the required data ahead of the course. Full details can be found on the [course webpage](video-analysis). If you encounter any issues, please contact Niko Sirmpilatze.
:::

Instructors: Niko Sirmpilatze, Chang Huan Lo, Sofía Miñano

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47 changes: 42 additions & 5 deletions docs/source/courses/video-analysis.md
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Expand Up @@ -24,12 +24,49 @@ This will cover how to run pose estimation at scale, using the GPUs of the SWC H
* [Sofía Miñano](https://github.com/sfmig)

## Prerequisites
Make sure to follow the [steps outlined here](https://github.com/neuroinformatics-unit/course-behavioural-analysis#prerequisites) which will guide you through
setting up your laptop, installing the required software, and downloading the sample data.

If you encounter issues with any of these steps please contact
<a href="mailto:n.sirmpilatze@ucl.ac.uk?subject=SWC/GCNU Software Skills">Niko Sirmpilatze</a>
in advance of the course.
### Hardware Requirements

This is a hands-on course, so **please bring your own laptop and charger**. A mouse is recommended but not essential. A dedicated GPU is not required but will be helpful.

### General Software Requirements

:::{note}
If you are an incoming PhD student attending the full [General Software Skills for Systems Neuroscience](general-software-skills) course and have already installed the general software requirements on Day 1, you may skip this section.
:::

- An IDE for Python programming. We recommend one of the following:
- [Visual Studio Code](https://code.visualstudio.com/) with the [Python extension](https://marketplace.visualstudio.com/items?itemName=ms-python.python)
- [PyCharm](https://www.jetbrains.com/pycharm/)
- [JupyterLab](https://jupyter.org/install)

- A working `conda` (or `mamba`) installation. If you don't have it, install via [Miniforge](https://github.com/conda-forge/miniforge).
- A working [Git](https://git-scm.com/) installation.

### Specific Software Requirements

:::{note}
Only proceed with this section after fulfilling the general software requirements above.
:::

You will need to pre-install two different `conda` environments for the practical exercises. Create them as follows:

1. [**SLEAP**](https://sleap.ai/): Use the [conda package method](https://sleap.ai/installation.html#conda-package) from the SLEAP installation guide. You may use either `conda` or `mamba` in the installation command. An NVIDIA GPU is not required for this course as you will only use the SLEAP GUI (launched using `sleap-label`).
2. [**Keypoint-MoSeq**](https://keypoint-moseq.readthedocs.io): Use the recommended [conda installation method](https://keypoint-moseq.readthedocs.io/en/latest/install.html#install-using-conda).

You should now have two new conda environments called `sleap` and `keypoint_moseq`. To view all your conda environments, run `conda env list`.

### Sample Data

Download the sample data for this course from [Dropbox](https://www.dropbox.com/scl/fo/ey7b6yrqax2olqyv1th7j/h?rlkey=u4wh2gxtbbn4g5o3s55zbx6pp&st=zolupk4i&dl=0). Click "Download" to get the `behav-analysis-course.zip` archive, then unzip it.

Alternatively, if you are connected to the SWC network and have access to the SWC's `ceph` filesystem, the dataset is available at `/ceph/scratch/neuroinformatics-dropoff/behav-analysis-course`.
Ensure you copy the data to a convenient location on your laptop.
The instructions to mount `ceph` on your laptop can be found on the [SWC wiki](https://wiki.ucl.ac.uk/display/SSC/Storage%3A+Ceph).

:::{note}
If you encounter any issues with these steps, please contact [Niko Sirmpilatze](mailto:n.sirmpilatze@ucl.ac.uk?subject=SWC/GCNU%20Software%20Skills) in advance of the course.
:::

## Materials
- [GitHub repository](https://github.com/neuroinformatics-unit/course-behavioural-analysis)
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