squirrel

Python-based library for conversion and processing of 3D EM data.

Installation via conda

hopefully coming soon:

conda create -n squirrel-env squirrel

Installation via pip

mamba create -n squirrel-env -c conda-forge python=3.11
mkdir path/to/src
cd path/to/src
git clone https://github.com/jhennies/squirrel
pip install -e squirrel

Installation of optional packages

Install the following as necessary to enable additional functionality

nibabel for handling nii files

This is required for 3D SIFT

mamba install -c conda-forge nibabel

Napari for 3D visualization

mamba install -c conda-forge napari pyqt

For registration

pip install SimpleITK-SimpleElastix
pip install transforms3d

also install OpenCV (see below)

OpenCV for 2D SIFT

mamba install -c conda-forge opencv

For ome.zarr support

mamba install -c conda-forge zarr

For faster filters or morphological operations

Note: this changes the numpy version!

mamba install -c conda-forge vigra

For MoBIE project support

mamba install -c conda-forge pandas

Usage

The main functions can be used directly after activation of the conda environment:

conda activate squirrel-env

compress_tif_stack -h
h5_to_tif -h
mib_to_tif -h
normalize_slices -h
tif_merge -h

The -h flag yields the help output describing functions and parameters