SLASH (System for Large-scale Automatic Segmentation utilizing High-performance computing techniques)

livewire

Implementation of the livewire algorithm that has speed and quality of results.

postprocess-chm-output

Scripts for the 3D post-processing of segmented image stacks

cytoseg

Automatically exported from code.google.com/p/cytoseg

DP2

Distributed Segmentation (using mturk)

HNS

Hierarchical Neuronal Segmentation

n15-pancreatic-islet

Files and scripts for the N15 pancreatic islet segmentation collaboration with Rafael.

segtools

Contains scripts to assist with the segmentation of EM data

stereopointcounter

Performs automated point counting stereology on greyscale probability maps

amiratools

Scripts for data import, morphological quantification, and movie generation using Amira

CCDB_ID_Generator_2021

Archive data and store metadata. Also generate the microscopy ID

CHM

Cascaded Hierarchical Model Automatic Segmentation Algorithm

chmimagedatasetfrommrc

Workflow to create CHM image dataset from MRC file using IMOD

chmimagedatasetworkflow

CHM Image dataset Workflow

chmtrainingdatasetworkflow

Kepler workflow that verifies data passed to it is in valid structure for CHM Train Workflow

chmtrainworkflow

CHM Train Workflow

chmworkflow

CIL_Public_Data_JSON

This repository contains all CIL public annotation metadata in the JSON format.

cookiecutter-keplerpython

cookiecutter template for a Kepler Workflow that runs a Python script via the Python Actor. Compatible with CRBS Workflow Service

cookiecutter-keplerunscript

Template for Kepler Workflow that generates a script and executes it. Compatible with CRBS Workflow Service

dropboxsharedlinkimport

This workflow takes a shared link from Dropbox and imports it into SLASH

exampleworkflows

Contains example Kepler Workflows compatible with CRBS Workflow Service

geoEM

Geometry analysis tools for segmented EM data

hubzero

hubzero cms, including component for crbs workflow service

imodfile

Verifies input WorkspaceFile is a valid IMOD model file

mrcfileworkflow

MRC File Workflow validates a MRC file

ncmirdataimport

Workflow to import data from NCMIR storage

PyCHM

Cascaded Hierarchical Model Automatic Segmentation Algorithm in Python

segmentertiledimage

Generates tiled images from Single Slice CHM image dataset workflow output

singlechmimagedataset

Extracts single slice from CHM image dataset workflow output

slashportal

Automatically exported from code.google.com/p/slashportal