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Benjamin D. Pedigo / Homepage / Twitter / Google Scholar

I am a Scientist at the Allen Institute for Brain Science, focusing on data science techniques for helping to understand nanoscale connectomes.

I did my PhD in the Deparment of Biomedical Engineering at Johns Hopkins University, advised by Joshua Vogelstein and Carey Priebe in the NeuroData lab. My thesis developed statistical and computational techniques for analyzing connectome data, and applied them to the connectome of an insect brain.

I am also a developer of graspologic (formerly called GraSPy), an open-source Python package for doing statistical analyses of network data which I now co-develop with Microsoft Research. I am broadly interested in making data analysis techniques in neuroscience more accessible through open-source software.

Ben Pedigo's Projects

apical_classifier icon apical_classifier

Tools for training and applying an apical classifier on skeleton data from the chunkedgraph

ardent icon ardent

Affine and Regularized DEformative Numeric Transform (ardent) is a Python package for performing image registration using LDDMM.

axon_id icon axon_id

Tools used in identifying the axons and dendrites of neurons

bdpedigo.github.io icon bdpedigo.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

cloud-workflow-mwe icon cloud-workflow-mwe

Minimal working example for cloud workflow using CAVE, Amazon SQS, Google Cloud Storage, etc.

cv icon cv

my curriculum vitae

fastpages icon fastpages

An easy to use blogging platform, with enhanced support for Jupyter Notebooks.

giskard icon giskard

A random collection of tools I find useful for data science.

graph-libs icon graph-libs

Stashing graph libraries I come across (mostly just Python ones)

graspologic-native icon graspologic-native

graspologic-native is a library of rust components to add additional capability to graspologic (https://github.com/microsoft/graspologic), a python library for intelligently building networks and network embeddings, and for analyzing connected data.

graspy icon graspy

Python package for graph statistics

imageryclient icon imageryclient

Publication-ready visualization of overlays of imagery and segmentation from cloudvolume data

lamination-evaluation icon lamination-evaluation

Analyzing the results of the 2024 "Best Croissant in Seattle" tournament from the Allen Institute Electron Microscopy Connectomics team

mesh-processing icon mesh-processing

Short scripts and functions for reading in binary meshes, downsampling if necessary, and exporting as .stl

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