Atlas: an Open-Source Software Package for Biological-Image Visualization

Atlas Figure1

Atlas is an open source software for 3D/4D/5D digital image visualization, analyzing fluorescence microscopy 2D & 3D image stacks, cell signals, visualizes various surface objects, digitally reconstructed neurons, 3D reconstruction, user-defined annotations in 2D & 3D space, brain modeling, image stitching, human MRI & MRA, and displaying fuctional biological-image data, etc.

We propose Atlas as a software for productive collaboration between biological research and bioimaging-informatics, and computer science communities.

It is available free in C source code format with some precompiled binaries for research purposes. Atlas SW Download is available for Mac OS, Windows, Linux

  • Open-Source
  • Simplist GUI
  • Easy of Use
  • User-Friendly Modern Graphical Interface
  • Seamless 2D & 3D Navigation
  • Image Stitching
  • Multithreaded, Image File Opening/Reading/Channels of Color Images Adjust/ Can Be Performed in Parallel
  • Allows Multiple Images to be Displayed on the Screen at One Time
  • Visualize the Large & Various File Formats in 2D & 3D Images
  • User Defined Selection can Calculate Area and Pixel Value
  • Concurrent Image, Annotation, and Viewing of Multiple Images - Click the Eye Button to Control the Concurrent Images
  • Multi-Channel with Various Beautiful Colors
  • 2D & 3D Video Recorder
  • Support 3D Image formats - DICOM, NIfTI, SWC, Tiff(.ome.tif, ome.tiff), RAW(.v3draw, .raw), HDF5img(.nim, .h5), jpeg, png, Kitware, MetaImage(.mhd, .mha), etc.

Compare to Other Well-Known Image Visualization Software,

  • Atlas is the simplest and easiest image visualization tool
  • Simple & Easy to use for First-Time Users
  • We focused on the User-Friendly Interface Design with the Full of Effort and Dedication

Atlas aims to provide useful functionality for a broad range of researchers, from programming-agnostic biologists to CS researchers. Atlas is for biologists who need basic as well as advanced image visualization. Atlas is one of tools developed by Korea Institute of Science and Technology(KIST), Brain Science Institute (BSI), Feng Lab.

Atlas Sample Video

  • Above video is made by Dr.Feng (PI, Atlas SW Developer)
  • If you are interested in making this video, see the tutorial part.

Quick Start Video

  • This screencast will help you get started or you can read our ‘Atlas Guideline’ below