Repositories list

• Membrane_Myelin_Subtract

  Public
  Subtract the Myelin layer from the All Membrane CDeep3M prediction

  PHP

  •

  MIT License

  •0•0•0•0•Updated Apr 1, 2025Apr 1, 2025

• CCDB_ID_Generator_2021

  Public
  Archive data and store metadata. Also generate the microscopy ID

  HTML

  •

  MIT License

  •0•0•0•0•Updated Jul 1, 2021Jul 1, 2021

• PyCHM

  Public
  Cascaded Hierarchical Model Automatic Segmentation Algorithm in Python

  Python

  •0•0•1•0•Updated May 30, 2018May 30, 2018

• CHM

  Public
  Cascaded Hierarchical Model Automatic Segmentation Algorithm

  Shell

  •

  BSD 2-Clause "Simplified" License

  •0•0•4•0•Updated May 30, 2018May 30, 2018

• segtools

  Public
  Contains scripts to assist with the segmentation of EM data

  Python

  •1•0•1•0•Updated May 23, 2018May 23, 2018

• geoEM

  Public
  Geometry analysis tools for segmented EM data

  C

  •0•0•0•0•Updated Apr 25, 2018Apr 25, 2018

• CIL_Public_Data_JSON

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

  2•0•0•1•Updated Apr 17, 2018Apr 17, 2018

• mrcfileworkflow

  Public
  MRC File Workflow validates a MRC file

  Shell

  •0•0•0•0•Updated Dec 29, 2017Dec 29, 2017

• chmimagedatasetworkflow

  Public
  CHM Image dataset Workflow

  Shell

  •0•0•0•0•Updated Dec 29, 2017Dec 29, 2017

• segmentertiledimage

  Public
  Generates tiled images from Single Slice CHM image dataset workflow output

  Shell

  •0•0•0•0•Updated Dec 29, 2017Dec 29, 2017

• chmtrainingdatasetworkflow

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

  Shell

  •0•0•0•0•Updated Dec 29, 2017Dec 29, 2017

• n15-pancreatic-islet

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

  Python

  •0•0•0•0•Updated Apr 27, 2016Apr 27, 2016

• amiratools

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

  Python

  •0•0•1•0•Updated Apr 26, 2016Apr 26, 2016

• slashportal

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

  HTML

  •0•0•0•0•Updated Mar 17, 2016Mar 17, 2016

• livewire

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

  C++

  •

  GNU General Public License v2.0

  •6•7•13•0•Updated Dec 17, 2015Dec 17, 2015

• ncmirdataimport

  Public
  Workflow to import data from NCMIR storage

  Shell

  •0•0•0•0•Updated Dec 8, 2015Dec 8, 2015

• postprocess-chm-output

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

  MATLAB

  •1•2•0•0•Updated Oct 28, 2015Oct 28, 2015

• stereopointcounter

  Public
  Performs automated point counting stereology on greyscale probability maps

  C++

  •0•0•0•0•Updated Sep 28, 2015Sep 28, 2015

• hubzero

  Public
  hubzero cms, including component for crbs workflow service

  HTML

  •0•0•0•0•Updated Sep 11, 2015Sep 11, 2015

• HNS

  Public
  Hierarchical Neuronal Segmentation

  C++

  •0•0•0•0•Updated Aug 18, 2015Aug 18, 2015

• dropboxsharedlinkimport

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

  Shell

  •0•0•0•0•Updated Aug 7, 2015Aug 7, 2015

• cookiecutter-keplerpython

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

  Shell

  •0•0•0•0•Updated Aug 3, 2015Aug 3, 2015

• imodfile

  Public
  Verifies input WorkspaceFile is a valid IMOD model file

  Shell

  •0•0•0•0•Updated Jul 31, 2015Jul 31, 2015

• cookiecutter-keplerunscript

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

  Shell

  •0•0•0•0•Updated Jul 29, 2015Jul 29, 2015

• singlechmimagedataset

  Public
  Extracts single slice from CHM image dataset workflow output

  Shell

  •0•0•0•0•Updated Jul 23, 2015Jul 23, 2015

• chmworkflow

  Public
  Shell

  •0•0•0•0•Updated Jul 16, 2015Jul 16, 2015

• chmimagedatasetfrommrc

  Public
  Workflow to create CHM image dataset from MRC file using IMOD

  Shell

  •0•0•0•0•Updated Jul 14, 2015Jul 14, 2015

• chmtrainworkflow

  Public
  CHM Train Workflow

  Shell

  •0•0•0•0•Updated May 28, 2015May 28, 2015

• exampleworkflows

  Public
  Contains example Kepler Workflows compatible with CRBS Workflow Service

  Shell

  •0•0•0•0•Updated Mar 20, 2015Mar 20, 2015

• cytoseg

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

  Python

  •1•0•2•0•Updated Mar 16, 2015Mar 16, 2015