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Software & Code

Available Software

AGAVE
Advanced GPU Accelerated Volume Explorer
Picture
​Description: The volume viewer uses path-trace rendering in an interface designed and optimized for the display of multi-channel OME TIFF files.
Requirements: This stable release requires a computer running the latest version of Windows 10 or Mac OS 10.12 or newer.
Instructions: Unzip the contents into a new directory on your Windows computer and open README.txt for detailed instructions to load and visualize volumetric data files.

Windows only: The first time you run AGAVE, if you see an error message about missing VCRUNTIME140_1.dll, then you need to download and install vc_redist.x64.exe from this link.  After the install, AGAVE should start normally.
Download AGAVE
AGAVE documentation
Help / Questions

What's New

November 12, 2020
  • scene selection dialog when opening multiscene files
  • added support for loading files with 8-bit intensities
  • new documentation
  • updated Qt to 5.15 LTS
  • minor bug fixes with JSON save and load
  • improved logging

Archived

Requirements: This ß release requires a computer running the latest version of Windows 10 or Mac OS 10.12 or newer.
Download AGAVE for Mac OS
Download AGAVE for windows

Available code

Analysis code for the manuscript Cell states beyond transcriptomics: integrating structural organization and gene expression in hiPSC-derived cardiomyocytes.
GitHub notebook for figures produced for the study.
The Allen Cell Structure Segmenter: a Python-based open source toolkit developed at the Allen Institute for Cell Science for 3D segmentation of intracellular structures in fluorescence microscope images.
Label-free Determination: Label-free prediction of three-dimensional fluorescence images from transmitted light microscopy
  • Label-free training data download
Integrated Cell: Image-driven generative cell modeling with adversarial autoencoders
Cell Shape Analysis Jupyter Notebook: What shape are our human induced pluripotent stem cells? Use a Jupyter notebook to help build intuition about shape across the population of cells available in the Allen Cell Collection.
Programmatic Data Access Jupyter Notebook: Learn how to download and access Allen Institute data using Quilt via a Jupyter Notebook.

More coming soon...

Our goal is to make all tools and software developed at the Institute publicly available once they are useful and robust. In the coming year, we will begin to post the code for various projects into open-source repositories.

​With a goal of practicing and promoting open science, we use and develop open-source software whenever possible and practical. Licensing will be described as the software is released.

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cellscience.alleninstitute.org
  • About
    • What We Do
    • FAQs
    • Videos & Tutorials
    • Site Updates
    • < Forum >
    • < AllenInstitute.org >
  • Animated Cell
    • Educational Resources
    • Visual Guide to Human Cells
    • Visual Guide Tutorial
    • Research Projects >
      • Pathtrace rendering
  • Cells & Biology
    • Cell Catalog
    • About our Cells >
      • hiPS Cell Biology Overview
      • Cell Structure Observations
      • Cell Catalog QuickView
    • Genomics
    • Methods & SOPs >
      • Methods for Cells in the Lab
      • Cell Methods: Videos from the Lab
      • Methods for Microscopy
    • Research Projects >
      • hiPS Cells During Mitosis
      • Drug Perturbation Pilot
      • Differentiation Into Cardiomyocytes
      • Why Endogenous Tagging?
  • Data & Tools
    • Cell Catalog
    • 3D Cell Viewer
    • Cell Feature Explorer
    • Integrated Mitotic Stem Cell Z-stack Viewer
    • Deep Cell Zoom
    • Segmenter
    • Data Downloading
    • Software & Code
    • Simularium
    • Research Projects >
      • Extracting Information
  • Modeling & Analysis
    • Integrated Mitotic Stem Cell
    • Allen Integrated Cell
    • Label-free Determination
    • Data Notebook Exploration >
      • Cell Shape Analysis
      • Programmatic Data Access
    • Research Projects >
      • 3D Probabilistic Modeling
  • News & Publications
    • News Feed
    • Publications
    • Archived Content