index.qmd

---
title: Software Skills for Systems Neuroscience
author: SWC/GCNU Neuroinformatics Unit
execute: 
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format:
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        date: "2024-02-12"
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---
# About us

## Neuroinformatics Unit
(Systems) neuroscience & machine learning **research software engineering** group

## Team{.smaller}
```{python}
#| output: asis
#| echo: false
images = [
    ("img/adam_tyson.jpg", "Adam Tyson"),
    ("img/laura_porta.png", "Laura Porta"),
    ("img/chang_huan_lo.png", "Chang Huan Lo"),
    ("img/joe_ziminski.png", "Joe Ziminski"),
    ("img/alessandro_felder.png", "Alessandro Felder"),
    ("img/niko_sirmpilatze.png", "Niko Sirmpilatze"),
    ("img/igor_tatarnikov.jpg", "Igor Tatarnikov"),
    ("img/sofia_minano.png", "Sofía Miñano")
]
n_per_row = 4
col_width = 80 / n_per_row
print(":::: {.row}\n")
for i, img in enumerate(images, start=1):
  src, caption = img
  print(f"::: {{.column width={col_width}%}}\n![{caption}]({src})\n:::\n")
  if i % n_per_row == 0 and i != len(images):
    print("::::\n:::: {.row}")
print("::::")
```

## What we do
:::{.incremental}
- **Data analysis software** (anatomy, electrophysiology, functional imaging, behaviour)
- **Data management** (specifications, tools)
- **Collaborations** (data science, software development, productionisation)
:::

## Current projects
:::{.incremental}
* Data standardisation and management
* Developer tools
* Modelling
* Extracellular electrophysiology analysis
* Video behavioural analysis
* Multiphoton analysis
* Computational neuroanatomy
:::

## More details
### [neuroinformatics.dev](https://neuroinformatics.dev/)

# The course

# Installation

{{< include slides/installation.qmd >}}

# Course details

## Course schedule{.smaller}

**Monday, September 30th**
- Introduction to Python (1)

**Tuesday, October 1st**
- Data management and sharing (1 & 2)

**Wednesday, October 2nd**
- Introduction to Python (2) & Version control and software development best practices

**Thursday, October 3rd**
- Video behavioural analysis (1 & 2)

**Friday, October 4th**
- Linux and high-performance computing

**Monday, October 7th**
- General microscopy & Histology analysis (1)

**Tuesday, October 8th**
- Histology analysis (2 & 3)

## Monday, September 30th{.smaller}

#### 13:00-17:30: Introduction to Python (1)
**Aims:** Run your first Python script and learn about variables, data types, loops and conditional statements in Python.

**Location:** SWC Brasserie Seminar Room

**Lead by:** Sofía Miñano, Igor Tatarnikov, Chang Huan Lo & Adam Tyson

## Tuesday, October 1st{.smaller}

#### 9:45-10:45: Data management and sharing (1)
**Aims:** Motivate the need for good neuroscience data management and introduce current best practices. 

**Location:** SWC Ground Floor Lecture Theatre

**Lead by:** Joe Ziminski, Niko Sirmpilatze

#### 15:00-17:30: Data management and sharing (2)
**Aims:** Learn our recommended data organisation principles and supporting software tools.

**Location:** SWC Ground Floor Lecture Theatre

**Lead by:** Joe Ziminski, Niko Sirmpilatze

## Wednesday, October 2nd{.smaller}

#### 10:00-12:30: Introduction to Python (2) 
**Aims:** Learn how to use third-party Python libraries, work with functions, classes, and objects, and handle exceptions in Python.

**Location:** GCNU Seminar Room

**Lead by:** Sofía Miñano, Igor Tatarnikov, Chang Huan Lo & Adam Tyson

#### 13:30-17:30: Version control and software development best practices
**Aims:** Learn how to keep track of changes to your code with Git and GitHub, work with others on code, and get an initial idea of how structure, document and test your code.

**Location:** GCNU Seminar Room

**Lead by:** Alessandro Felder, Laura Porta, Steve Lenzi

## Thursday, October 3rd{.smaller}

#### 10:00-13:00: Video behavioural analysis (1)
**Aims:** Introduction to the theory and practice of tracking animals in videos, including hands-on training of pose estimation models.

**Location:** SWC Brasserie Seminar Room

**Lead by:** Niko Sirmpilatze, Sofía Miñano, Chang Huan Lo

#### 14:00-17:30: Video behavioural analysis
**Aims:** Using Python to analyse animal tracks produced via pose estimation: cleaning data, quantifying movement, extracting behavioural syllables.

**Location:** SWC Brasserie Seminar Room

**Lead by:** Niko Sirmpilatze, Sofía Miñano, Chang Huan Lo


## Friday, October 4th{.smaller}

#### 14:00-17:30: Linux and high-performance computing
**Aims:** To learn some basic principles of high-performance computing (HPC), and run a specific workflow on the SWC HPC system

**Location:** SWC Ground Floor Lecture Theatre

**Lead by:** Niko Sirmpilatze, Igor Tatarnikov, Adam Tyson

## Monday, October 4th{.smaller}

#### 11:00-12:00: General microscopy: basics
**Aims:** Learn basic concepts about microscopy to enable specific histology analyses

**Location:** SWC Brasserie Seminar Room

**Lead by:** Rob Campbell

#### 13:00-14:30: General microscopy: applications
**Aims:** Learn basic concepts about microscopy to enable specific histology analyses

**Location:** SWC Brasserie Seminar Room

**Lead by:** Rob Campbell

#### 14:30-17:30: Histology analysis (1)
**Aims:** Introduce napari and the BrainGlobe ecosystem of tools along with some basic image analysis concepts

**Location:** SWC Brasserie Seminar Room

**Lead by:** Alessandro Felder, Igor Tatarnikov, Adam Tyson


## Tuesday, October 5th{.smaller}

#### 10:00-11:00: Histology analysis (2)
**Aims:** Learn how to register whole brain microscopy data to an atlas, and analyse structures within the images.

**Location:** SWC Ground Floor Lecture Theatre

**Lead by:** Alessandro Felder, Igor Tatarnikov, Adam Tyson


#### 14:00-17:30: Histology analysis (3)
**Aims:** Learn how to detect cells in large images, and analyse and visualise the results

**Location:** SWC Ground Floor Lecture Theatre

**Lead by:** Alessandro Felder, Igor Tatarnikov, Adam Tyson

## Full details
[software-skills.neuroinformatics.dev/courses/software-skills](https://software-skills.neuroinformatics.dev/courses/software-skills.html)

### Any questions?