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AGAVE 3D pathtrace image viewer

​Introducing AGAVE
Advanced GPU Accelerated Volume Explorer


Visualization advances for enhancing spatial relationships
 

Try the full AGAVE pathtrace viewer on your desktop

What's New in AGAVE v1.4.0   |  June 30th, 2022
  • ROI sliders now show pixels/slices for precise positioning, and have draggable bars
  • Volume scale gets more decimal places
  • Fix issue loading some CZI time series
  • Improve TIFF loading of xy pixel scale in non-OME tiffs
See our announcement on image.sc forum!
​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, or can be built from GitHub source for Linux.
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.
Picture
Available for Windows & MacOS
Download AGAVE
AGAVE documentation
GitHub
Help / Questions

Try a simple pathtrace viewer directly in your browser

  1. Visit the Cell Feature Explorer, click on any dot in the plot to load a cell into the gallery.
  2. Click on any cell in the gallery to load it into the online 3D volume viewer at the bottom of the page. 
  3. Click the [Path trace] button at the upper left.
  4. Turn on all Volumes in the Segmentation channels and turn off all volumes in the Observed channels as a starting point.
  5. Adjust the transfer function graphs to find an ideal setting.
Cell Feature Explorer with pathtrace
Picture

Visualization Advances for Enhancing Spatial Relationships… Even Online

Most volumetric visualization tools that cell biologists use have evolved from 2D image analysis predecessors. They provide powerful analysis capabilities, especially for looking at one slice of a 3D volume or a projection, but they have limited 3D visualization functionality. Transforming a stack of 2D slices into a 3D volume and then interactively rotating it makes complex spatial relationships easier to see and understand.

The most common 3D volume rendering methods make the stacked image slices transparent so the observer can see through the entire volume. However, this can compromise the appearance and detail of the signal (Fig. 1A). Users can adjust the transparency to make denser voxels (the 3D analog to pixels) stand out, but this rendering approach is far removed from how we view and intuitively interact with everyday objects, lacking, for example, any concept of a directional light source, adjustable highlights, or shadows that can help us intuit complex topologies and distance relationships. The volumes can require longer interactions and more experience to interpret, and it can be impossible to correctly interpret depth relationships if the user cannot interactively rotate the volume, for example if it is displayed on a printed page.

New approaches to rendering volumes are being adapted and developed for use in cell biology to help us literally see the cells in a more familiar and thus intuitive manner. For example, by adopting approaches such as “cinematic rendering” techniques to cellular volumetric data, one can see fine details become more visible and spatial relationships more interpretable, even in a 2D static printed image (Fig. 1B). This makes exploring cellular data more analogous to dissecting a cadaver rather than looking only at x-ray projections when learning human anatomy. These types of approaches should become an important addition to the arsenal of visual analysis tools needed to study and see a cell from every possible perspective and in every possible way. This cinematic approach can also be adjusted to emulate the method shown in (a) when transparency is useful.
Picture
Figure 1: Live hiPS cells in a monolayer are labeled for the cell boundary (magenta), DNA (cyan), and microtubules (white). Cells are imaged in 3D using spinning disk confocal microscopy and the image is displayed with: a) the most common type of volume rendering method as in this example from www.allencell.org/3d-cell-viewer.html; and b) newly adopted “cinematic lighting” techniques to volume rendering in development at the Allen Institute for Cell Science. 

Download AGAVE from the Software page
Available for Windows & MacOS

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

Download AGAVE for Mac OS
Download AGAVE for Mac 0.9.0.0
Download AGAVE for windows
Download AGAVE for Windows 0.9.0.0

What's New

March 30, 2020
  • Transfer function editor
  • Time series support (loads one time sample at a time)
  • Embedded Python and Python script export
  • Miscellaneous UI improvements
  • Zeiss CZI file support​

Try the full viewer on your desktop

Picture
Software Download page
The AGAVE viewer is available for Mac and Windows operating systems, and can be built from source for Linux. AGAVE uses path-trace rendering in an interface designed and optimized for the display of multi-channel OME TIFF files.

For this v1.0 release, we provide documentation for using AGAVE to help you explore its capabilities. 

Archived

This beta release of the AGAVE viewer is available for Mac and Windows operating systems. The volume viewer used path-trace rendering in an interface designed and optimized for the display of multi-channel, single-time OME TIFF files.

After the v1.0 release, we will provide tutorials for using AGAVE, but the current distribution offers a readme file to help you explore preview of the capabilities.

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  • About
      Institute
      1. News feed
      2. What we do
      3. Publications
      4. Allen Institute | allenInstitute.org
      5. Careers
      Site
      1. Home page
      2. Site updates
      3. Archived content
  • Allen Cell Collection
      Order cells & plasmids
      1. Cell Catalog
      2. Cell Catalog quickview
      3. Cell Shorts (documentaries on labs using our cells)
      4. Support forum
      Lab methods
      1. Instructional videos for success in the lab
      2. Standard operating procedures (written methods)
      3. Illustrated overviews
      About our hiPS cells
      1. hiPS Cell Structure Overview
      2. Visual Guide to Human Cells
      3. Cell structure observations
      4. Why endogenous tagging?
      5. Differentiation into cardiomyocytes
      6. Genomics
      7. Download cell data (images, genomics, features)
  • Data & Digital Tools
      Online image analysis
      1. Cell Feature Explorer (plotting & 3D viewer)
      2. 3D cell viewer (pre2018)
      3. Deep cell zoom (216,016 cells)
      Online modeling viewers
      1. Visual Guide to Human Cells
      2. Simularium (4D visual analysis)
      3. Integrated Mitotic Stem Cell
      4. └ Z-stack viewer
      5. └ 3D viewer
      6. Allen Integrated Cell viewer
      7. Label-free examples viewer
      8. 3D probabilistic model viewer
      Desktop tools
      1. Allen Cell & Structure Segmenter
      2. AGAVE 3D pathtrace image viewer
      Data & code
      1. Download cell data (images, genomics, features)
      2. Code repositories & software
  • Analysis & Modeling
      Allen Integrated Cell models
      1. Overview
      2. Integrated Mitotic Stem Cell
      3. └ Z-stack viewer
      4. └ 3D viewer
      5. Label-free Determination
      6. └ 3D viewer
      7. 3D Probabilistic Modeling
      8. └ 3D viewer
      9. Visual Guide to Human Cells
      4D biology models
      1. Simularium (online 4D viewer)
      Methodologies
      1. Drug perturbation pilot study
      2. hiPS cells during mitosis
      3. Differentiation into cardiomyocytes
  • Publications
      Articles
      1. All journal publications
      2. Preprints (biorxiv, arxiv)
      Posters
      1. Select posters
  • Education
      Education resources
      1. All Resources
      2. Teaching materials
      Online tools popular with teachers
      1. Visual Guide to Human Cells
      2. Integrated Mitotic Stem Cell
      3. Cell Feature Explorer (interactive plotting & 3D viewer)
      4. 3D cell viewer (pre2018 data)
      5. hiPS cell structure overview
  • Support
      Questions
      1. FAQs
      2. Forum
      Tutorials for digital tools
      1. Digital tool tutorials with videos
      2. Visual Guide tutorial
      3. AGAVE user guide
      Lab methods
      1. Instructional videos for success in the lab
      2. Standard operating procedures (written methods)
      3. Illustrated overviews
  • 🔍
      SEARCHBAR