COE Technology list - hedwig pipelines

[philipmac]

Utils (RML HPC - AKA BigSky)
imod, v4.10.48.37755
IMOD is an open-source, cross-platform suite of modeling, display and image processing programs used for 3D reconstruction and modeling of microscopy images with a special emphasis on electron microscopy data.

ffmpeg, v2.8.15
FFmpeg is the leading multimedia framework, able to decode, encode, transcode, mux, demux, stream, filter and play pretty much anything that humans and machines have created.

ImageMagick, v6.9.10-68
ImageMagick, invoked from the command line as magick, is a free and open-source cross-platform software suite for displaying, creating, converting, modifying, and editing raster images.

Python Packages

prefect, v1.4.1
Prefect is a modern workflow orchestration tool for coordinating all of your data tools

dask, v2023.5.1
Dask is a flexible open-source library for parallel computing

distributed, v2023.5.1
Dask Distributed extends Dask to run on HPC clusters

dask-jobqueue, v0.8.1
Runs Dask jobs on job queuing systems like PBS, Slurm, MOAB, SGE, LSF, and HTCondor.

natsort, v8.3.1
A package that contains a function that sorts "naturally". The EM users tend to name files in awkward ways, however there are patterns and an order. natsort() gets these patterns correct. (The files must be read in according to a specific order.)

pytools, v2.0
A collection of python utility functions that assist image processessing for Hedwig workflows - authored by Brad Lowekamp et al.

SimpleITK, v2.2.1
An interface to ITK, authored by Brad Lowekamp et al

numpy, v1.24.3
Numerical computing tools.

zarr, v2.14.2
A package that can process Zarr.

SimpleITKUtilities v0.1.0
Ancillary utils which enhance the basic SimpleITK Python package functionality, authored by Brad Lowekamp et al