Retrieval and analysis of connectomics data from different EM data sets
- To have a google (e.g., gmail) account
- To have high motivation and self-learning capabilities
- To be open to do pair-coding
ENVIRONMENT MANAGER
- Download and install anaconda (or miniconda) from: https://docs.anaconda.com/anaconda/install/
GIT
- Download and install git from: https://git-scm.com/
INITIALIZE ENVIRONMENT The anaconda prompt or the git bash terminals can be used. In the git bash though, anaconda environments need to be set as source, running:
source C:/Users/[USERNAME]/anaconda3/Scripts/activate
In any of those terminals, follow the commands:
- conda create --name <env_name> python=3.9
- activate <env_name> (-- FOR ACCESSIND DATA VIA NEUPRINT --)
INSTALL PACKAGES FOR DEALING WITH EM DATA SETS
- pip install neuprint-python
- pip install navis
- pip install fafbseg
CHECK IF THE FOLLOWING PACKAGES ARE INSTALLED, IF NOT, INTALL THEM
- pip install numpy
- pip install pandas
- pip install matplotlib
- pip install seaborn
- (other packages might be needed)
OPTIONAL RECOMENDED PACKAGES
- pip install notebook (for Jupyter Notebooks)
IMPORTANT CONSIDERATIONS
- Since NeuPrint is working with a google account (Gmail or similar). If you are any jupyter notebook in the browser, it is better to use google chrome. For that, google chrome needs to be the default browser option in the computer.
OPEN A JUPYTER NOTEBOOK
- Typer "jupyter notebook" in the <env_name> environment prompt
- Look for the notebook file (.ipynb) and open it
OPTIONALLY, OTHER TEXT EDITORS CAN BE USED THAT HANDLE COMPLEX FILE TYPES:
- Atom: https://atom.io/
- VSCode: https://code.visualstudio.com/
OR SIMPLER TEXT EDITORS, SUCH US:
- Vim (no installation needed)
- Nano (no installation needed)