FED3
FED3 or Feeding Experimentation Device Version 3 is a home cage feeding device, developed by the Kravitz Lab.
It is open source and is used for the training of mice in operant tasks.
Purpose
The CSV output from the FED3 devices show the timestamps of each event, like nose pokes or pellet retrievals. This repository :
- Converts this output into a time binned file. It also adds another sheet with the time stamps of all pellet count changes.
- Creates a master file that combines all the “Left poke count” columns from the raw FED files into one sheet. It does the same thing for the other column types as well. The columns are then sorted by genotype and treatment.
Preview of the graphical user interfaces
Input and output data
Install Anaconda Navigator.
Open Anaconda Prompt (on Mac open terminal and install X-Code when prompted).
Download this repository to your home directory by typing in the line below.
git clone https://github.com/Andrews-Lab/FED3_time_bins.git
If you receive an error about git, install git using the line below, type "Y" when prompted and then re-run the line above.
conda install -c anaconda git
Verify that Git was installed correctly:
git --version
Change the directory to the place where the downloaded folder is.
cd FED3_time_bins
Create a conda environment and install the dependencies.
conda env create -n FTB -f Dependencies.yaml
Activate the environment.
conda activate FTB
Open Anaconda Prompt (on Mac open terminal).
Change the directory to the place where the git clone was made.
cd FED3_time_bins
Activate the conda environment.
conda activate FTB
Run the codes.
python FED.py
If you encounter errors about missing packages, you can install them manually. For example, the project requires PySimpleGUI v4.60.5 (the newer v5.x versions may cause licensing or attribute errors). Install it using the line below.
conda install -c conda-forge pysimplegui=4.60.5
Verify that PySimpleGUI installed correctly:
python -c "import PySimpleGUI as sg; print(sg.version)"
You should see: 4.60.5
If you see errors about other missing modules (e.g. PyYAML), you can install them using the lines below.
conda install -c conda-forge pyyaml
or
pip install pyyaml
If your environment becomes corrupted, you can delete and recreate it using the lines below.
conda deactivate
conda remove --name FTB --all
conda env create -n FTB -f Dependencies.yaml
conda activate FTB
View the guide about how to analyse your FED data.
Authors:
Harry Dempsey, Taaseen Rahman
Credits:
Zane Andrews, Wang Lok So, Lex Kravitz, Taaseen Rahman
About the labs:
The Andrews lab investigates how the brain senses and responds to hunger.
The Foldi lab investigates the biological underpinnings of anorexia nervosa and feeding disorders.
The Kravitz lab investigates the function of basal ganglia circuits and how they change in diseases such as obesity, addiction, and depression.