Have you ever wanted, but lacked the time, to learn Python programming to update your data analyses and perhaps enhance them with new tools? In this era where open science is increasingly promoted, we are offering you the opportunity, over the course of two days, to delve into Python and its free tools. The idea behind this project is primarily collaborative; we aim to share our programming expertise to support you in what can sometimes be a long and challenging learning process. The objective is simple: by the end of these two days, we hope to provide you with a better understanding of Python’s role and value, help you begin transitioning some of your scripts and analysis methods, and offer suggestions to improve your workflows. For this project, no prerequisites or prior documentation are required. We will provide you with an interface and a ready-to-use environment so you can start programming, even from scratch. We look forward to seeing you motivated and eager to join this project. If you have any datasets you'd like to work on, feel free to bring them along, and we’ll be here to guide you. Get ready for coding!

Getting use to Python and overall OpenScience, understand the different roles and interests of Python programming in scientific studies, be proud of your own code.

1. A suitable and functioning Python environment (code environment, coding interface …)

2. Know where to find informations, and solve code issues

3. Know the good practices

https://mattermost.brainhack.org/brainhack/channels/bhg2024_wise-project

Learn to use the Python language in the broad outlines, to be able to perform your own analyses and scripts (Statistics, Data exploration, Preprocessing, Automation, Machine learning, Regression …)

Feel free to bring your own datasets, and suggest your own analysis interest.

more

All contributors are listed on the project's README.md file.

coding_methods, pipeline_development

0_concept_no_content

other

Jupyter, other

Python

other

0_no_git_skills

• What are you doing, for whom, and why?
  Our team develops the brain-SLAM python package designed for analyzing neuroimaging data using surface-base approaches. We improve it during hacking sessions and welcome external contributors!
• What makes your project special and exciting?
  The project is at an intermediate stage: not brand new but still not mature enough for spreading the world, let's move on!
• How to get started?
  Send an email to guillaume.auzias-at-univ-amu.fr
• Where to find key resources?
  https://brain-slam.github.io/slam/
  https://github.com/brain-slam/slam

https://github.com/brain-slam/slam

• Update continuous integration tools using github actions
• Improve code testing and quality
• Propose new features
• Improve our coding skills
• Work collaboratively
• Have fun

1. any kind of unitest

2. any kind of tutorial

Will setup one on site

• Content and current status of brain-SLAM
• Collaborative work

Example data already included in the repos.

3

All contributors are listed on the project's README.md file. We will also discuss the writing of a paper.

method_development

2_releases_existing

other

other

Python

MRI

2_branches_PRs

Macapype is pipeline wrapping several software commands in order to segment non human Primate MR images. However in some cases, one of those command fails due to some extreme bias present in the images acquired with some high multidimensional array whose elements are small and in close proximity of the anatomy to be imaged. In some cases, when the vitamin pastille is close to the antenna, it is hyper intense and the usual commands for registering the images to the template fail.

https://github.com/Brainhack-Marseille/brainhack-marseille.github.io/issues/new?assignees=&labels=project&template=brainhack-project-template-2024.yml

We expect to robustify Macapype with respect to images with strong receive bias.

1. Visit this page for description of the origin of the problems encountered with those kind of acquisition:
   https://github.com/PRIME-RE/prime-re.github.io/wiki/NHP-Issues

https://mattermost.brainhack.org/brainhack/channels/bhg24-marseille

• bash
• FSL
• ANTs
• NiftyReg
• Python

When participating to this project, you will learn about MR images artifacts and how to correct them.

NHP data acquired from the CERMED can be used, also

1

All contributors are listed on the project's README.md file.

method_development, pipeline_development

0_concept_no_content

MR_methodologies

ANTs, FSL, Nipype, other

shell_scripting, unix_command_line

MRI

1_commit_push

eLab is an electronic laboratory notebook for researchers. Which is useful for the acquisition of different experimental data/ metadata. Its aim is to no longer use a paper laboratory notebook and digitalize all the metadata related to experiments. This is useful for the data acquisition process by researchers. Also important in the data standardization process.

https://github.com/elabftw/elabftw

The aim is the presentation of an electronic laboratory notebook: eLab. Allowing the acquisition of experimental data/ metadata. This presentation will be followed by a general discussion on the use of laboratory notebooks and how to use them.

https://mattermost.brainhack.org/brainhack/channels/bhg24-marseille-elabftw

1. Electronic lab notebook
2. Different ways to use it

more

Every collaborator will have equal credits.

other

0_concept_no_content

other

other

not_applicable

not_applicable

0_no_git_skills

I aim to investigate calcium activity in two types of glial cells—radial glia (RG) and astrocytes—surrounding the central canal of the spinal cord. This region is known for its strong rhythmic activity, driven by neurons with high rhythmogenic capabilities, which arise from both intrinsic and network properties. These neurons are surrounded by astrocytes, which play a regulatory role in their rhythmogenic activity (Barbay et al., 2023). Additionally, research from Arulkandarajah et al. (2021) has shown that RG exhibit calcium spikes, unlike astrocytes. The key question is: How do radial glia and astrocytes interact during locomotion, and how do they influence pacemaker neurons in the spinal cord? This project seeks to uncover how glial cells contribute to the rhythmic dynamics of the spinal cord, offering insights into their roles in locomotion.

https://github.com/beyondNeurons/beyondNeurons

To characterize the spatiotemporal dynamics of calcium signaling in these two glial cell types within the lumbar spinal cord.

1. WP1: Segmentation of calcium imaging data to identify radial glia and astrocytes
2. WP2: Analysis of the area under the curve (AUC) of calcium transients under three conditions:
• C1: Baseline (ACSF)
• C2: TTX treatment to block neuronal activity
• C3: TTX combined with a locomotor cocktail
3. WP3: Mapping the spatial distribution (xy positions) of active astrocytes relative to the central canal

https://mattermost.brainhack.org/brainhack/channels/bhg24-marseille-beyondNeurons

This project seeks to uncover how glial cells contribute to the rhythmic dynamics of the spinal cord, offering insights into their roles in locomotion.
The participants will learn (i) how to do segmentation of cell subtypes, (ii) exctraction and analysis of two-photon calcium imaging data, and (iii) locate active cells in a 2D field of view.

3

Co-authorship.

pipeline_development

1_basic structure

physiology

other

Python

other

4_not_applicable

2P calcium imaging