Software

Seung Lab develops, maintains, and uses a variety of open-source software. Below is a partial list of the softwares with their corresponding links.

 

cnpkg (Srini Turaga) – A package for Cortical Network Simulator by Jim Mutch, which is a framework for the fast simulation of cortically-organized networks on CUDA-capable NVIDIA GPUs. cnpkg enables the creation of 3D convolutional networks and also trains them via the backpropagation algorithm. cnpkg was used to train the convolutional networks used in our published retinal reconstructions (Helmstaedter et al., 2013 and Kim et al., 2014). It has been superseded by ZNN.

JavaScript / jQuery library (William Silversmith and Mark Richardson) – A library used in EyeWire with various features, including color representation switches, dynamic triggers, and throttled rendering.

jQuery DLay plugin (Mark Richardson) – A jQuery plugin used in EyeWire that adds XHR chaining ability. Provides chaining wrappers for jQuery’s AJAX methods and for XHR request, serializing every request in the same queue. Progress and load events are available with reports for active request progress and total queue size. Supports serial or parallel queues.

rgc (Uygar Sümbül) – Implements the methods described in “A genetic and computational approach to structurally classify neuronal types,” Nature Communications, 2014.

Trainable Weka Segmentation (Ignacio Arganda-Carreras) – A Fiji plugin that combines a collection of machine learning algorithms with a set of selected image features to produce pixel-based segmentations using Weka. Provides a framework to use and compare any available classifier to perform image segmentation based on pixel classification, bridging machine learning and image processing. Has GUI support. 

Watershed (Aleksandar Zlateski) – Modified watershed segmentation used in EyeWire.

ZNN (Aleksandar Zlateski) – Multi-CPU core implementation of convolutional networks in 2D and 3D, including FFT and direct convolution, as well as max filtering.

VAST (Daniel Berger) – Volume Annotation and Segmentation Tool for manual annotation of large EM stacks.