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=2

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

For VSNR

pip install pyvsnr

Usage

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

conda activate squirrel-env

sq-conversion-cast_dtype -h
sq-mobie-export_rois_with_mobie_table -h
sq-serialem-parse_navigator_file -h
sq-stack-clahe_on_stack -h
sq-stack-estimate_crop_xy -h
sq-stack-invert_slices -h
sq-conversion-cast_segmentation -h
sq-mobie-init_project -h
sq-stack-axis_median_filter -h
sq-stack-compress_tif_stack -h
sq-stack-filter_2d_workflow -h
sq-stack-normalize_slices -h
sq-conversion-n5_to_stack -h
sq-serialem-create_link_maps -h
sq-stack-calculator -h
sq-stack-crop_from_stack -h
sq-stack-get_label_list -h
sq-stack-tif_nearest_scaling -h

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