Skip to content

@CRBS Center for Research in Biological Systems

Change the repository type filter

All

    Repositories list

    37 repositories

    • chmutil

      Public
      Utilities to run Cascaded Hierarchical Model (CHM) jobs on cluster of computers
      Python
      •
      Other
      •1•0•7•14•Updated Nov 24, 2024Nov 24, 2024

    • CIL_Image_Viewer

      Public
      This image viewer utilizes the Leaflet library and the CodeIgniter PHP library for browsing the high definition images.
      HTML
      •
      MIT License
      •0•3•0•0•Updated Oct 31, 2024Oct 31, 2024

    • CIL_PHP_Website

      Public
      Display data using Elasticsearch and utilize the bootstrap layout
      HTML
      •
      Other
      •2•5•47•1•Updated Sep 17, 2024Sep 17, 2024

    • Biological_Imaging_Methods_Ontology

      Public
      A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.
      Creative Commons Attribution 4.0 International
      •2•1•2•1•Updated Oct 18, 2023Oct 18, 2023

    • CIL_Metadata_Forms

      Public
      This app provides the metadata input forms for the CIL.
      HTML
      •
      MIT License
      •0•0•0•0•Updated Sep 28, 2023Sep 28, 2023

    • cildata_util

      Public
      CIL Data Extraction Utility to download/convert data from legacy CIL website
      Python
      •
      Other
      •0•0•2•4•Updated Dec 26, 2022Dec 26, 2022

    • cdeep3m2

      Public
      Plug-and-Play deep learning for image segmentation of large-scale microscopy data
      Shell
      •
      Other
      •4•7•3•10•Updated Nov 22, 2022Nov 22, 2022

    • CIL_RS

      Public
      PHP
      •
      Other
      •0•2•0•0•Updated Oct 28, 2021Oct 28, 2021

    • Image_Viewer_Data_Converter

      Public
      Scripts for converting images to the compatible format for the CIL Image Viewer
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 20, 2021Oct 20, 2021

    • cdeep3m

      Public
      Please go to https://github.com/CRBS/cdeep3m2 for most recent version
      Shell
      •
      Other
      •10•58•2•0•Updated Feb 9, 2020Feb 9, 2020

    • nbcrtrainingvm

      Public
      Contains a vagrant configuration to generate a virtual machine with software needed for NBCR summer training class
      Shell
      •0•0•0•0•Updated Jul 24, 2018Jul 24, 2018

    • probabilitymapviewer

      Public
      Probability Map web viewer
      Java
      •0•2•1•0•Updated Jul 24, 2018Jul 24, 2018

    • multicolor_em

      Public
      ImageJ plugin to overlay color-coded nanoSIMS/EELS chemical maps over the Conventional EM images
      Java
      •0•0•0•0•Updated Jul 24, 2018Jul 24, 2018

    • cildatatiler

      Public
      Shell
      •0•0•0•0•Updated Jun 12, 2018Jun 12, 2018

    • chm_singularity

      Public
      Generates Singularity image for Cascaded Hierarchical Model (CHM)
      Shell
      •
      Other
      •0•0•1•0•Updated May 11, 2018May 11, 2018

    • ncmirtools

      Public
      Commandline tools for NCMIR
      Python
      •
      Other
      •0•1•4•0•Updated Apr 3, 2018Apr 3, 2018

    • Panfish

      Public
      Multicluster job submission
      Perl
      •0•0•7•0•Updated Aug 22, 2017Aug 22, 2017

    • puppet-nbcrtrain

      Public
      Puppet configuration to configure a Linux Centos machine with software needed for NBCR summer training course
      Puppet
      •
      Other
      •0•0•0•0•Updated Jul 4, 2017Jul 4, 2017

    • etspecutil

      Public
      A set of utilities to run ET-SPEC (formerly known as Etphantom) from the command line
      Python
      •
      Other
      •0•0•0•0•Updated Mar 30, 2017Mar 30, 2017

    • segmask

      Public
      Masks a stack of segmented images into individual IMOD model files
      Python
      •0•2•0•0•Updated Aug 11, 2016Aug 11, 2016

    • PyIMOD

      Public
      A set of Python classes that enable the manipulation of IMOD model files.
      Python
      •2•3•2•0•Updated Aug 10, 2016Aug 10, 2016

    • morphome

      Public
      Run organelle-specific morphometric analysis and visualization workflows by interfacing with Amira.
      Python
      •0•1•0•0•Updated Aug 10, 2016Aug 10, 2016

    • autodockjobgenerator

      Public
      AutoDockWrapper is a command line java application that generates Auto Dock jobs from a set of ligands and receptors that can be run directly or via Panfish on compute clusters.
      Java
      •0•0•0•0•Updated Mar 7, 2016Mar 7, 2016

    • cws

      Public
      CRBS Workflow Service -- Is a REST Service to enable execution of Kepler Workflows via Panfish
      Java
      •0•0•8•0•Updated Dec 8, 2015Dec 8, 2015

    • openldap

      Public
      Pascal
      •1•0•0•0•Updated Oct 27, 2014Oct 27, 2014

    • role

      Public
      Puppet
      •0•0•0•0•Updated Oct 24, 2014Oct 24, 2014

    • core_firewall

      Public
      Core firewall module. This module sets up the basic firewall. This module also is a wrapper/supplement for the main firewall module provided from forge.puppetlabs.com
      Puppet
      •1•0•0•0•Updated Oct 21, 2014Oct 21, 2014

    • motd

      Public
      Puppet MOTD Module
      Puppet
      •8•0•0•0•Updated Oct 17, 2014Oct 17, 2014

    • yumrepos

      Public
      Yum repository classes for Puppet
      Puppet
      •16•0•0•0•Updated Oct 10, 2014Oct 10, 2014

    • beanstalk_console

      Public
      Admin console for Beanstalk queue server
      JavaScript
      •214•0•0•0•Updated Nov 19, 2013Nov 19, 2013