Fluorender

This is the open-source repository for FluoRender, an interactive tool for fluorescence microscopy data visualization and analysis.

<h1 id="download">Download</h1>

Download the installer package for your operating system (OS).

| 🖥️ Windows (10 and 11, 64-bit, x86_64 CPUs) | 🍎 Mac OS (13.3+, M1, M2, etc. CPUs)| 🍎 Mac OS (13.3+, Intel CPUs) | 🐧 Linux | |------------|-----------|----------|----------| | Version 2.34 | Version 2.34| Version 2.34 | Email me |

Support the maintenance and bug fixes by donnation: https://paypal.me/fluorender

<h1 id="features">Release Highlights for Version 2.34</h1> FluoRender’s new release comes from a year of rethinking the project’s purpose and focusing entirely on what biologists actually need, leading to major upgrades in mesh speed, rendering quality, and overall usability. A new GPU‑based mesh generator, modernized lighting, a rebuilt framebuffer system, smarter multichannel intermixing, cleaner color‑mapping, clipping boxes for meshes, and a suite of new analysis tools all grew naturally from that shift in direction. The release also introduces a brand‑new DICOM reader, rounding out a version shaped by experimentation, refinement, and a renewed sense of why FluoRender exists in the first place.

• Looking Glass Support

  • FluoRender now supports both volume data and mesh objects on the latest Looking Glass holographic displays, expanding your visualization toolkit with intuitive controls and immersive clarity.
  • The 16" Looking Glass displays can be purchased here: https://lookingglassfactory.com/looking-glass-16-lightfield
  • The 27" Looking Glass displays can be purchased here: https://lookingglassfactory.com/looking-glass-27
  • And a portable holographic display, the Looking Glass Go can be purchased here: https://lookingglassfactory.com/lkg-go

• Mesh & Surface Improvements

  • Much faster mesh generation using a new GPU based method.
  • Cleaner, more modern mesh appearance with updated lighting and shadows.
  • Clipping boxes now work for meshes, with options to sync across objects.
  • New mesh analysis tools: volume, surface area, smoothing, simplification, welding.
  • 4D mesh generation and playback for time series data.
  • Real time mesh creation with paint and grow brushes.
  • Color transfer from components to meshes for easier segmentation workflows.

• Volume Rendering & Visualization

  • Updated lighting for volumes (softer shadows, clearer structure).
  • More reliable multichannel intermixing — all combinations now behave sensibly.
  • Brush selected and unselected regions can use different color modes.
  • New “no display” mode for hiding unselected regions.
  • MIP now works with color maps and depth mixing.

• Color Mapping Enhancements

  • Two new color maps: radial and linear.
  • Color maps now align with data, not just axes (PCA based by default).
  • Color gradients can follow any measurement tool or viewing direction using the probe tool.

• System & Performance Upgrades

  • Major framebuffer redesign for more predictable rendering and faster effects.
  • More intuitive shader system for both volumes and meshes.
  • Smoother interaction when mixing render modes, effects, and color maps.

• New Data Format Support

  • DICOM reader.

<h1 id="documentation">Documentation</h1>

User Manual: Version 2.34

Tutorials: Version 2.34

Video Tutorials: YouTube Playlist

<h1 id="contact">Contact</h1>

Contact the developer for any questions or suggestions:

Email: yong.wan@utah.edu

Facebook Page: FluoRender on Facebook

<h1>Hardware Requirements</h1>

FluoRender can run on most personal computers including desktops and laptops. The key component is a modern GPU (Graphic Processing Unit). A powerful GPU is helpful to process large data.

<h1>Aknowledgments</h1>

<strong>Code Contributors: </strong> Yong Wan, Brig Bagley, Takashi Kawase, Remaldeep Singh, etc.<br/> If you use FluoRender in work that leads to published research, we humbly ask that you add the following to the 'Acknowledgments' section of your paper: "This work was made possible in part by software funded by the NIH: Fluorender: Visualization-Based and Interactive Analysis for Multichannel Microscopy Data, R01EB023947." If you would like to cite FluoRender, you may reference the following publication: Wan, Y., et al. (2017). FluoRender: joint free-hand segmentation and visualization for many-channel fluorescence data analysis. BMC Bioinformatics, 18:280.

<h1>Building FluoRender</h1> <h2>Common Dependencies</h2>

Some third-party dependencies are included in the FluoRender source code. Other dependencies need to be prepared before building FluoRender. This is especially true after recent reoganization of FluoRender source code, as many dependencies are moved out of the project. They need to be built or installed before building.

• Windows 10 and later : Visual Studio 2017 and later<br/>
  • Or Mac OS 11 (Big Sur) and later : Updated Xcode and command line tools<br/>
  • Or Ubuntu Linux 22.04 (tested to work)
• Git (https://git-scm.com/) for managing the source code
• CMake (http://www.cmake.org/) for generating building projects
• Boost (http://www.boost.org/users/download/#live) for computing using the graph library
  • Needs building before FluoRender
• Dlib (http://dlib.net) for deep neural network calculations
  • No need to build before FluoRender for the template library
• FFmpeg for reading and writing video files
  • https://github.com/FFmpeg/FFmpeg.git
  • x264 codec (https://code.videolan.org/videolan/x264.git)
  • x265 codec (https://bitbucket.org/multicoreware/x265_git.git)
  • May need MSYS2 to build on Windows
  • Build codecs first and then FFmpeg
• FreeType for managing type fonts
  • https://github.com/freetype/freetype.git
  • Needs building before FluoRender
• GLEW (https://glew.sourceforge.net) for OpenGL extension management
  • https://github.com/nigels-com/glew/releases/tag/glew-2.2.0
  • Needs building before FluoRender
• GLM for mathematics like vectors, matrices, and quaternions
  • https://github.com/g-truc/glm.git
  • No need to build for header-only library
• HDF5 (https://www.hdfgroup.org/download-hdf5/) for managing HDF files
  • https://github.com/HDFGroup/hdf5/releases/tag/hdf5_1.14.5
  • Needs building before FluoRender
• JDK (https://www.oracle.com/java/technologies/downloads/) for linking to ImageJ functions
  • Needs installation
• OpenBLAS for linear algebra computations
  • https://github.com/OpenMathLib/OpenBLAS.git
  • Needs building before FluoRender
• OpenCL SDK for cross-platform GPU computing
  • There are multiple providers. On Windows, I use NVIDIA CUDA Toolkit:
  • https://developer.nvidia.com/cuda-toolkit
  • Needs installation
• OpenCV (https://opencv.org/) for computer vision calculations
  • https://github.com/opencv/opencv.git
  • Needs building before FluoRender
• OpenJPEG for reading DICOM files compressed with JPEG 2000
  • https://github.com/uclouvain/openjpeg.git
  • Needs building before FluoRender
• OpenVR (https://steamvr.com) for SteamVR headset support
  • https://github.com/ValveSoftware/openvr.git
  • Needs building before FluoRender
• OpenXR (https://www.khronos.org/openxr/) for OpenXR headset support
  • https://github.com/KhronosGroup/OpenXR-SDK.git
  • Needs building before FluoRender
• Python (https://www.python.org/downloads/) for linking to Python functions
  • Needs installation
• Teem (https://teem.sourceforge.net/) for reading and writing Nrrd format files
  • Needs building before FluoRender
  • I maintain a repo here: https://github.com/basisunus/teem.git
• wxWidgets (https://github.com/wxWidgets/wxWidgets) for user-interface library
  • I made some changes to the wxWidgets code. Use my custom branch
  • I generally use the built-in libs in wxWidgets, including Jpeg, Png, Tiff, etc.
  • Needs building before FluoRender
• Zlib (https://github.com/madler/zlib.git) for reading compressed data formats
  • Needs building before FluoRender

Libraries that need building before FluoRender or included as head-only are placed at the same level of the FluoRender source code path so that they can be automatically found. See FluoRender's CMake file for more details. I usually prefer the source code of a released version instead of the master head.

<h2>Linux</h2>

1. Make sure OpenGL and OpenCL drivers are correctly installed and configured. This is OS and hardware dependent.

   Libs needed: libOpenCL1, glu-devel; headers needed: opencl-headers.

2. Other dependencies include: gcc, g++, gtk3-devel, ffmpeg-4-libavcodec-devel, ffmpeg-4-libavformat-devel, ffmpeg-4-libavutil-devel, ffmpeg-4-libswscale-devel, ffmpeg-4-libswresample-devel, etc.

3. Clone and build boost.

   • <code>git clone --recursive https://github.com/boostorg/boost.git</code>