mfishtoolspy

• Tools to analysis mFISH data, including gene panel selection from reference dataset.
• This is a python version of https://github.com/AllenInstitute/mfishtools with slight modifications
  • Bootstrapping instead of subsampling
  • Multiple iterations (default=100) per gene addition instead of single random seed to increase reliability across repetition
  • Parallel computing using dask
  • Some functions are not included yet. (e.g., fraction_correct and dendrogram_height optimization)
• This is still in active development (as of 12/10/2024)

How to install

pip install mfishtoolspy

Or

git clone https://github.com/AllenNeuralDynamics/mfishtoolspy.git
cd mfishtoolspy
pip install -e .