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

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    33 repositories

    • 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•7•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

    • DP2

      Public
      Distributed Segmentation (using mturk)
      Python
      •0•0•0•0•Updated Dec 12, 2013Dec 12, 2013