Installation Guide

Note

Since zoom involves the processing and integration of multiple modalities of data, a relatively large number of Python packages are involved. Installation via pip will only automatically include those packages essential for the core workflow of zoom. Nevertheless, during development, we also prepared several functions for the preprocessing of spatial brain phenotypes (SBPs) and single-cell RNA sequencing (scRNA-seq) dataset, which necessitate the configuration of additional Python packages or the setup of an R environment.

Installation requirements

zoom was developed and tested using Python 3.9. Backwards‑compatibility and forwards‑compatibility with other Python 3 versions are expected but not guaranteed. All Python package version dependencies are handled automatically if installing zoom via pip (as described below).

• Python 3

Python packages for data processing:

• numpy

• pandas

• nibabel

• scanpy

• sklearn

• scipy

• statsmodels

Python packages for parallel computation:

• joblib

• tqdm

Dependencies

In addition to the Python packages listed above, we also prepared several functions for the preprocessing of spatial brain phenotypes (SBPs) and single-cell RNA sequencing (scRNA-seq) dataset. If you hope to prepare anatomically comprehensive Allen Human Brain Atlas (AHBA) gene expression profile optimized for cortical samples, please install abagen. Additionally, if you hope to preprocess SBPs and implement spatial permutation test, please also install neuromaps. We also provided python interface for running hdWCNA, if needed, please set up appropriate R environment following the guidance of hdWCNA tutorial.

Installation

zoom can be downloaded from GitHub repository:

$ conda create -n zoom_env python=3.9
$ conda activate zoom_env
$ cd ZOOM-main

Install other requirements:

$ pip install -r requirements.txt

Install zoom:

$ pip install .