Fluorescence Microscopy

Designed especially for neurobiologists,
FluoRender is an interactive tool for multi-channel
fluorescence microscopy data visualization and analysis.


Previous Versions

Sample Data


Advancing Microscopy with FluoRender


01 Clonal Units in Drosophila Brain 02 Study of Mouse Limb Anatomy
03 Study of Clonal Units in Drosophila Brain 04 Study of Zebrafish Visual System
05 Analysis Functions 06 OpenCL Programming Interface
FluoRender is an interactive rendering tool for confocal microscopy data visualization. It combines the rendering of multi-channel volume data and polygon mesh data, where the properties of each dataset can be adjusted independently and quickly. The tool is designed especially for neurobiologists, allowing them to better visualize confocal data from fluorescently-stained brains, but it is also useful for other biological samples.

Please cite the following publication:
FluoRender: joint freehand segmentation and visualization for many-channel fluorescence data analysis. Yong Wan, Hideo Otsuna, Holly A. Holman, Brig Bagley, Masayoshi Ito, A. Kelsey Lewis, Mary Colasanto, Gabrielle Kardon, Kei Ito and Charles Hansen.  BMC Bioinformatics, 18:280, 2017. DOI 10.1186/s12859-017-1694-9

FluoRender User's Guide (PDF)

FluoRender Tutorials (PDF)

10/17/2016. Ver 2.20 released !!

New Features:

  • Clustering algorithms. Three clustering algorithms for segmentation are added: expectation-maximization on Gaussian mixture, DBSCAN, and k-means. Users can use these methods in the "Component" window.
  • Improved tracking algorithms. Tracking accuracy has been improved. We improved the algorithm for generating the track map and incorporated clustering algorithms to automatically segment during tracking. Users can also adjust a series of parameters in the "Tracking" window to fine tune the tracking.
  • A new 4D script for tracking sparse particles. The 4D script allows users to track selected features in a time sequence. No initial segmentation is required for it to work. It can be used to track sparse and small features conveniently.
  • A density setting for component generation. The density setting has been added in the basic component generation. Its concept is based on the clustering algorithm DBSCAN. However, its implementation is based on the synthetic brainbows algorithm, which uses GPU to compute segmentation of dense data sets.
  • Render view output enlargement. The option has been added when the render view is captured and saved as an image. Users can set an output image size larger than the render view size.
  • 4D script list. The list of built-in 4D scripts has been added to the "Record/Export" panel. Users can easily select and switch 4D scripts without browsing to the actual files.

The 2.20 release of FluoRender also fixed these issues:
  • An issue that changed render view zoom factor when setting key frames.
  • An issue of reading Prairie/Bruker xml formats, when the TIFF files were saved/processed by third-party tools.
  • An issue that paint brush was not working properly on the latest AMD graphics cards.
  • An issue that component generation failed on the latest AMD graphics cards.
  • An issue that certain volume property settings became unavailable when switching between MIP and normal render modes.
  • An issue that render view became blank or corrupted on Mac OS X Yosemite.
  • Other minor issues of the user interface.

Release Notes
Known Issues
FluoRender License
FluoRender Acknowledgement

Release notes: 4/20/2016 FluoRender 2.19
FluoRender 2.19 has a number of improvements, bug fixes and new features:

Bug Fixes

  1. Insufficient slicing numerical precision that might cause artifacts due to misalignment.
  2. It read hidden files as part of a sequence on Mac OS X.
  3. Problems to read time sequence data correctly.
  4. It sometimes cleared a selection mask when paint brush history was recalled.
  5. Selection mask operations from the tracking dialog were not registered in the paint brush history.
  6. Empty groups were left unused when several data sets were repeatedly loaded and deleted.
  7. Clipping patterns when many channels were rendered with microblending.
  8. The bitrate setting for QuickTime movie export was not working on Mac OS X.
  9. FluoRender settings were not read and saved correctly on Mac OS X.
  10. Issues of the user interface.

New Features

  1. Support of OpenCL 1.2. Please make sure the latest graphics driver is installed. Deprecated functions from OpenCL 1.1 have been updated in FluoRender to work with OpenCL 1.2.
  2. A new setting for render view text color. It allows more flexible customization of the color of render view text, including the scale bar. You can choose to use the background color, the inverse of background color, or the secondary color of a volume channel.
  3. A new 4D script type for executing OpenCL filters. It allows application of an OpenCL filter to each file of a time sequence. Use this function for image processing of a time sequence.
  4. Improved main tool bar for analysis tools. The last used analysis tool will be displayed on the main tool bar, allowing easy access to the tool.
  5. A new component analysis module. It manages all settings and analysis functions.
  6. A new external executable for applying component analysis settings to a time sequence. It can read settings from the new component analysis module and then apply them to an input file. Use this feature along with the 4D script for external executable to apply component analysis to a sequence of files.
  7. New OpenCL filters. Two OpenCL filters are included for computing morphological gradient and Sobel edge detection.
  8. An option to save the alpha channel in screenshots. You can choose to save an additional alpha channel in screenshots, so that the captured images can be used in a compositing software.
  9. An uncertainty analysis on tracking results. You can analyze an automatic tracking result and locate uncertain tracks. Use this feature to manually fix tracking issues with good efficiency.
  10. A mode switch for zoom ratio display. You can choose how the zoom ratio is displayed. Two modes are available. The first mode is view-based, where the percentage of the zoom ratio value represents the size of an entire data set to that of the render view. The second mode is data-based, where the zoom ratio value represents the rendered size of a data set to its 1:1 voxel-pixel state.
  11. Synchronization of individual volume property settings. Volume property settings can be individually synchronized within a group. Double-click a property’s name to synchronize.

    • Many of the bug fixes, improvements, and new features became available because of the cordial support from FluoRender users. We wish to thank every user and welcome any suggestions for future releases.


Release notes: 10/30/2015 FluoRender 2.18
FluoRender 2.18 has a number of improvements, bug fixes and new features:

Bug Fixes

  • Micro blending was not working in the Depth channel intermixing mode.
  • The selected part of a labeled volume was not displayed correctly in the Depth channel intermixing mode.
  • An issue in the track map file when two components were linked backwards in time.
  • A transient ruler was not shown at the correct sequence time point when the batch mode was enabled.
  • Refresh issues when the volume rendering was configured to draw from front to back.
  • All channels could not be loaded from a sequence of RGB TIFFs when the batch mode was enabled.
  • The application crashed when first a channel had been deleted and then played back a sequence in the batch mode.
  • An output frame was missing when the last key only was consisted of one frame in the advanced output panel.
  • The visualization of a volume data set disappeared at certain viewing angles in the free fly mode.
  • Issues of the user interface.

New Features

  • Improvements to automatic tracking
    Tracking quality has been improved in the 2.18 release of FluoRender. A new function is added to allow automatic refinement on only one time point.
  • Manual tracking and automatic-manual mixed tracking
    A complete set of manual tracking functions is back and reorganized in the user interface. Automatic and manual tracking can be used separately or jointly. You can use manual tracking functions to fix the issues in the result from automatic tracking, or use automatic tracking to refine partial result from manual tracking. Certain operations, such as ID assignment and linking can be automated even in full manual tracking for a streamlined workflow.
  • Analysis and conversion tools for tracking results
    You can convert a tracked trajectory to a ruler, or assign consistent IDs to a series of tracked components. A new script is added to allow visualization of all tracked components. You can get information about selected components as well as the number of broken and multiple links in the tracking results.
  • Smooth interpolation for rotation movie export
    You can choose linear or smooth interpolation in the basic movie export panel for rotations.
  • Surface area calculation for mesh objects
    When you convert a volume or its selected part into a mesh object, it reports the surface area of the resulting mesh object.
  • Full screen mode
    You can turn on the full screen mode so that a render view port occupies the entire display area. This is a feature only available on Microsoft Windows.
  • Clipping plane display modes
    You can hold the display of the clipping planes of a volume, so that they can be viewed when you move the mouse cursor outside of the clipping plane panel area. In addition, there are five modes for displaying clipping planes.
  • New keyboard shortcuts
    Several new keyboard shortcuts are added, including clearing selection and time sequence play back.
  • Two selectable rotation slider modes
    You can select how the rotation sliders in the render view panel control view rotations. The first mode is a “steering wheel” that rotates the view continuously, where the rotation speed is controlled by the slider thumb button’s displacement. The second mode directly sets the rotation angle by the button’s displacement.
  • Edge strength setting for paint brush
    A new setting for the paint brush allows you to adjust how strong a gap between two structures is considered as an edge. When edge detection is enabled for paint brush, this new setting allows finer control of selection region.


  • For Windows7+, download the win64 EXE file and run the setup. You may need to allow security settings to run the installer. Please be sure to read and accept the Licence.
  • For OSX10.9+, download the osx DMG file. Open the archive and drag the FluoRender icon to the Applications shortcut. You may need to replace a previous version. You may also need to allow security settings to run the program (Settings, Security, Open Anyway). Please be sure to read and accept the Licence.

Release notes: 8/25/2015 FluoRender 2.17
FluoRender 2.17 has a number of improvements, including bug fixes and added features.

New Features

  • History for paint brush operations
  • A secondary color setting for volume data
  • Choice of color maps and color map modes
  • Protractor tool
  • Separation of non-overlapping samples into channels
  • Recording channel intermixing modes
  • Baking clipping planes
  • A new 4D script type for executing an external application from FluoRender
  • Automatic tracking

Bug Fixes

  • Fixed several issues of reading files (mostly unicode related)
  • Using the paint brush tool in streaming mode had issues that are fixed.


  • For Windows7+, download the win64 EXE file and run the setup. You may need to allow security settings to run the installer. Please be sure to read and accept the Licence.
  • For OSX10.9+, download the osx DMG file. Open the archive and drag the FluoRender icon to the Applications shortcut. You may need to replace a previous version. You may also need to allow security settings to run the program (Settings, Security, Open Anyway). Please be sure to read and accept the Licence.

Release notes: 5/27/2015 FluoRender 2.16

We are excited to announce the 2.16 release of FluoRender. For Microsoft Windows users, FluoRender 2.16 incorporates minor feature improvements and issue fixes. However, we have upgraded all graphics functions, conforming to the OpenGL core profile specifications. It allows us to have continuous support for future graphics processing units. FluoRender 2.16 requires graphics cards with a minimum support of OpenGL 3.3. Older graphics hardware need to be replaced. For Apple Mac OS X users, there is the exciting news that all features previously exclusive to Windows are now available*. It still requires relatively recent Apple hardware (2009 and on) and the operating systems.

These issues were fixed:
1. It sometimes did not read an LZW-compressed, RGB channel TIFF file correctly.

These improvements were included:
1. The calculation of the depth attenuation has been improved, which is based on the data size from current viewing direction. A higher contrast can be achieved by increasing the attenuation factor. The depth attenuation effect now also supports mesh data.
2. It allows users to change the text and color of measurement tools, including locators and rulers.
3. It supports True-type fonts in the render view. You can change the settings for font and size in the setting dialog. You can also copy your own True-type font file to the installation directory to let FluoRender use it.
4. OpenGL core profile version and GLSL version can be selected in the FluoRender setting file.
5. The documentation of tutorials was updated to include new features as well as a chapter on movie export.

* Ten-bit output requires capable hardware and may not be available for Apple computers.

Note: FluoRender 2.16 was officially announced on May-26, 2015. We had put a test version on-line earlier than this date, so that the new functions, especially on Mac OS X, could be tested. If you happen to download the 2.16 version prior to the official release, please download it again.

Last but not least, we would like to thank Ken Calderone from the University of Michigan, who suggested the improvements including modifiable text for measurement tools, font, and text size settings. We appreciate the continuous support from our users. Please let us know if you have any comments.

Release notes: 1/27/2015 FluoRender 2.15.2

These issues were fixed:
1. It failed to read a TIFF file with multiple strips when saved with LZW compression.
2. Memory leaks when multiple GPUs were installed and an OpenCL kernel was used.
3. A volume data set could not be compressed with OpenGL RG texture compression.
4. The application icon looked jagged under Windows.
5. Rulers were not saved in a project file.
6. Applying paint brush strokes on a data set larger than 4 GB caused FluoRender to crash. After fixing, it performs best on the latest graphics cards with 12 GB of memory (Geforce GTX Titan X or Quadro K6000).

These improvements are included:
1. When the keyboard shortcuts for the paint brush tool are used, it allows single mouse clicking to select/unselect a circular region.
2. Speed of applying a paint brush stroke is significantly improved, especially for large data on slow computers.

These new features are included:
1. A probe tool to create a two-point ruler along the viewing direction. When used in combination with the paint brush tool (via key board shortcut), it creates a cylindrical selection along the ruler.
2. A profile tool to calculate intensity profiles along rulers. This tool is best used along with the probe tool to generate an averaged intensity profile within the cylindrical mask region.

Release notes: 1/27/2015 FluoRender 2.15.1

This version fixed a bug in FluoRender 2.15, which wrote a blank frame when exporting movies in QuickTime MOV format. However, we also incorporated these new features and improvements:
1. Automated key generation for advanced movie making
2. A 10-bit output option for compatible professional graphics hardware (an AMD FirePro or Nvidia Quadro graphics card connected with a 10-bit capable LCD display via DisplayPort)
3. Antialiasing options for compatible graphics cards
4. Automatic cropping in movie making/image capturing
5. Minor UI improvements

For more details, please read FluoRender User's Guide, which can be accessed
within FluoRender or downloaded along with FluoRender.

Release notes: 12/29/2014 FluoRender 2.15

New Features
1. OpenCL kernel editor. New in the 2.15 release of FluoRender, an OpenCL kernel editor is added to the tool collection. The editor can be accessed from menu->Tools->OpenCL kernel editor. It allows users to create, load, edit, and save an OpenCL kernel for 3D image processing. Active kernel is applied to selected channel when the "Run" button is pressed. A list of built-in kernels are also provided for basic 3D filtering operations. See Chapter 19 of the user's manual for more details.
2. Automatic threshold estimation for paint brush. New in the 2.15 release of FluoRender, threshold for paint brush can be estimated by applying brush strokes. The estimation is based on the local histogram of the data under the first applied stroke. Its calculation is performed with an OpenCL kernel. See Chapter 14 of the user's manual for more details.

Improvements include UI updates and bug fixes. More importantly, we edited a user's manual that covers all the latest features of FluoRender in great detail.

Release Notes: 10/09/2014 FluoRender 2.14

This version has expanded to MacOSX, includes improved user interface, issue fixes, and other program improvements.
1. Simplified and more user-friendly Recorder Dialog Box.
2. Icon-based options, Program File Menu, Optional Toolbar, and more intuitive controls.
3. More support for various TIF file formats.
4. Output of Quicktime MOV format available for recording.
5. Support for larger data sets. (Option available in Settings).
6. New 3D Measurement and Ruler Tools (for lengths, position, etc.)
7. Key Framing available for Advanced recording.
8. Continuous perspective angle adjustment.
9. Additional shortcut buttons for clipping planes/slabs.
10. New tracking tool to track structures in 4D time sequence data.

FluoRender 2.13

This version includes some improvements and issue fixes:
1. File loading speed for TIFF format is improved. For 4D playback, the speed increase can be 100% on certain systems. For the best speed performance, save a 4D sequence in separate, uncompressed channels.
2. When saving projects, there is an additional option for embedding datasets into the project directories. However, complete 4D sequence will not be saved using this feature.
3. Rendering contrast is increased for fine details with less opacity, when a bright background color is used.
4. It also includes other minor fixes with user interface, etc.

FluoRender 2.12

This version includes some improvements and issue fixes:
1. The colormap legend reflects transparency settings, which is more accurate to visualized results.
2. Fixed an issue in gradient magnitude calculations.
3. Added interpolation option in the render view settings. It turns on/off interpolations on the current selection.
4. Alpha in the volume property settings can be turned on/off.
5. Selection in the workspace panel is linked in the datasets panel.
6. A compression option is available in the open volume dialog. It reduces graphics memory usage and improves rendering speed.
7. Fixed some issues for Olympus format reading.
8. In the edit window, an edge detection option is added to the selection adjustment section. It enables the brush to use gradient magnitude for edge detection.
9. In the edit window, a select group option is added to the selection adjustment section. It allows painting on all channels in one group simultaneously.
10. Other minor user interface improvements and issue fixes.

FluoRender 2.10.1

1. In the edit dialog, removed 2D adjustment influence slider.
2. When growing region is turned off, selection is based on intensity thresholding.
3. Re-organized the property window for polygon mesh, with lighting being a feature that can be turned on/off.
4. Added a setting in the settings dialog. It allows ignoring voxel size from metadata.
Issues Fixed: 
1. When voxel size of XY plane is not set to 1, The 1:1 button won't zoom current dataset correctly. This is now fixed.
2. After loading polygon mesh files several times, they may all disappear.  This is now fixed.
3. In certain situations, the workspace panel become empty after loading a project. This is now fixed.
4. The setting for saving LZW compressed TIFFs is not saved properly. This is now fixed.

FluoRender 2.10.0

New Features:
1. Volume baking.
2. A link to FluoRender's facebook page.
1. Support of LZW compressed Olympus formats (OIB and OIF).
2. Save TIFF files (screen captures or volume data) with LZW compression.
3. Polygon mesh can be selected by mouse click in the render views.
4. Name of current selected data can be displayed in the render view.
5. Many UI improvements.
Issues Fixed:
1. Low intensity voxels can be selected by setting a low falloff value of volume paint selection.
2. Larger paint stroke can have stronger grow strength. 
3. Faster rendering of time sequence data through fixing a bug in using graphics memory.

FluoRender 2.9.1

This version has some issues fixed and improvements on usability.
1. Fixed a sampling rate issue when a volume is anisotropic and user sets XY spacings much greater (or smaller) than 1.
2. Users can choose a gradient background from the settings dialog.
3. Progress is shown when reading data or projects.
4. Improved user interactions when user chooses to use the workspace toolbar for volume painting functions.
5. Volume data loaded in the datasets panel can be saved as a sequence of 2D TIFF files.

FluoRender 2.9.0

New Features:
1. Interactive volume segmentation.
2. Calculations between two volumes (Addition, Subtraction, Division, and And).
3. Derived volumes from the above operations can be saved as multi-layer Tiffs from the Datasets panel.
1. A 2D Tiff sequence can be opened as a volume. The new option is in the open volume dialog.
2. Users can set the 4D time sequence identifier in the open volume dialog.
3. Better LSM format support, including support of larger-than-4GB 4D data.
4. Excitation wavelengths can be read from raw format meta data and used for default color settings.
5. Improved polygon mesh rendering speed.
6. Better OBJ format support.
7. Automatic search for broken-link files when project and data are copied to a different directory.
8. Improved shadow effects.
9. Shadow effects in Depth render mode.
10. Instant render view update for most numeric inputs.

FluoRender 2.8.0

New Features:
1. Support of importing several manufacturer-specific confocal formats, including Olympus Image Binary (*.oib), Olympus Original Imaging Format (*.oif), and Zeiss Laser Scanning Microscope (*.lsm).
2. Variable sample rate for mouse interactions.
3. Equalization for equalizing uneven brightness of 3D and 4D data. It also enhances details at the same time.
4. Shadow effects and directional shadows.
1. Improved user interface. Panels can be hidden or shown with a toolbar button.
2. Installation packages for FluoRender setup.
3. FluoRender project files (*.vrp) are associated with the executables if FluoRender is installed with the installation package. Double-clicking the project files will automatically launch FluoRender.
4. Project files as well as volume datasets can be drag-and-drop to either the FluoRender icon or the main interface to open.

FluoRender 2.7.0

New Features:
1. Rendering core rewritten, for better rendering quality and performance.
2. True 16 bit TIFF support. Parameter settings reflect the actual scalar values.
3. Real-time smoothing filters for reducing the artificial patterns.
4. Data within groups can be set to depth mode, even the viewport is set to layer or composite mode.
5. Micro Blending. It can render accurate colors of multiple channels in depth mode, with an arbitrary number of channels.
6. User can set the zoom to reflect 1:1 voxel to pixel ratio.
7. One dataset can be added multiple times for renderings, and each instance can have independent parameter settings.
1. Several user interface and parameter setting improvements, for better usability.
2. In MIP mode, and colormapped MIP mode, some parameters are disabled, in order to keep the color accuracy.
3. Rendering quality and speed for mesh and mesh with volume improved.
1. The four modes for gradient magnitude calculation settings are removed.
2. User can set the mesh rendering quality by adjusting the number of layers to render.

FluoRender 2.6.1

New Features:
1. A 64bit version can run on 64bit Windows systems. It supports loading larger
2. Maximum Intensity Projection (MIP) mode can be selected for any volume
channels from the volume properties. Shading effects, intensity-dependent
colormap, and most volume properties are also supported in MIP mode.
3. The clipping planes can be rotated independent of dataset rotations. The
user can set the clipping plane rotations either by aligning to view, or by
adjusting explicit rotation angles.
4. The clipping planes are color-coded.
5. The confocal voxel size can be retrieved from TIFF metadata, if presented.
6. A new option for saving a project file during image/movie export.
7. The time range can be set for 4D sequence movie export.
8. FluoRender now has a Twitter page, which can be accessed from the main

FluoRender 2.5.0

New Features:
1. Realtime multi-channel 4D rendering with full playback control.
2. 3D batch rendering for RGB multi-layer TIFF files. Switching between multi-channel datasets is easy and fast.
3. Scalar value dependent colormap. The colormap is a blue-green-red gradient for low to high scalar values.
4. RGB multi-layer TIFF format support. RGB multi-layer TIFF files are added to the render view automatically after opened.

1. Property settings of datasets within the same group can be synchronized through the Tools panel.
2. Camera position and rotation are saved before switching to Free Fly mode, and they are restored after switching back to either Perspetive or Orthogonal projections.
3. Tools panel has less blinking when volume data are selected.

Issues Fixed:
1. The visibility status of the groups are saved in the project files.
2. Solved an OBJ mesh file reading problem.
3. Solved a clipping plane setting by numeric input problem.
FluoRender 2.4.0

New Features:
1. 4D multi-channel rendering.
2. New rendering modes that calculate the gradient magnitude differently. Choose different modes in the settings dialog can balance between rendering speed, data loading speed, and memory usage.
3. Saved volume properties can be set by the new reset button in the Tools panel.
4. The number of reset buttons of the 2D adjustment panel is reduced to three.

Issues Fixed:
1. When new data are added to the group with existing volumes, the voxel size of the newly added volume is set to the existing ones.
2. Less crash when open project file with existing volumes.
3. Transparency of the volumes is corrected when open project files with Depth mode.
4. Color icons of the volumes in the scene view are corrected to always follow their color settings.
5. Same dataset in different render modes look the same now.

FluoRender 2.2.0

New Features:

1. Drag & drop support in the tree of the scene view. User can now drag & drop items in the scene view to re-order and re-group them. The order of the volume data will be shown in the layered mode.
2. Groups in the tree of the scene view. Volume datasets can be grouped by creating new groups and dragging into the groups. Volume data in the same group share the same 2D adjustment parameters.

1. Spin buttons added for rotation settings.
2. For movie capture, the value for reverse rotation is always considered as the absolute value, no matter what the user input is.
3. 2D adjustment channel linking is automatically calculated from the color settings. Non-zero RGB channels will be linked in the 2D adjustment settings, when user changes the color of the volume data.
4. It remembers the HSV values of the volume data before user sets luminance. So the hue and saturation of the volume data will not change when user changes the luminance value within the range [0, 255].

Bugs Fixed:
1. In previous versions, the scaling of the volume datasets will change after viewport resizing. The problem is now fixed.
2. In previous versions, the program will crash sometimes when user deletes volume datasets from the data view. The problem is now fixed.
3. In previous versions, the program crashes quite often when loading volume datasets with slice resolution equal or larger than 1024x1024. Now the problem is fixed.

FluoRender 2.0.0

New Features:
1. Gamma and brightness adjustment for final results.
2. Save settings as default for render view.
3. Preview, stop, and reset angel for movie export.
4. XYZ rotation reset button, and spin buttons for finer control.
5. Double-click to trun channel display on/off in the scene view panel.
6. Color representations for channels in scene view.
7. In property panel, volume XYZ voxel ratio are set without hitting "Enter" key.

Issues fixed:
1. 32-bit transparency blending for better detailed structures.
2. Slicing distance recalculated for consistent transparency during rotation.

FluoRender 1.2.0

New features:
1. Scale bar for size reference. The length, unit and text of the scale bar can be set by the user. The length of scale bar is linked to viewport zoom. Though scale bar is available for perspective projection, it's recommended that use it in orthographic mode for accuracy.
2. Clipping planes. Clipping planes can be set for different channels independently, or they can be linked for all the channels.

Issues fixed:
1. Zoom of render view is calculated according to the relative size of the dataset bounding box to the viewport, rather than previously the projected voxel size to screen pixel size. Thus even datasets acquired with different objectives and scanning resolutions can generate comparable rendered results, with zoom being set to similar values.

FluoRender (ß) 1.1.0

Fixes to lighting problems when rotating the datasets.

FluoRender (ß) 1.0.9

Bugs fixed:
1. Switching render mode when the viewport is empty causes crash.
2. New channels added to the viewport don't show up in "Depth Mode".
3. Viewport flickering when changing the render modes.

New features:
1. Rotation animation and movie export.
2. Viewport rendering supports perspective and orthographic projections.
3. Double-click/Enter to add opened datasets to the viewport.

FluoRender (ß) 1.0.8

1. Fixes to some memory leaks.
2. Rendering speed is improved in "Depth Mode".
3. Fixes to image distortion of viewport capturing on some systems.
4. Fixes to program crash when capture viewports.

1. When using large data set option, the paintbrush is not available.
2. Paintbrush and related tools (including tracking) are unavailable for MacOSX.
3. Equalization in the Output Adjustment panel is unavailable in MacOSX.
4. Some large data sets have been known to crash the program on smaller graphics cards.
5. Minor bugs exist in a few tools. Please report any issues that affect your FluoRender experience.

FluoRender is available for free and is open source under the MIT License

The MIT License Copyright (c) 2012 Scientific Computing and Imaging Institute, University of Utah. License for the specific language governing rights and limitations under Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

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, 1R01EB023947-01 and the National Institute of General Medical Sciences of the National Institutes of Health under grant number P41 GM103545-18"


Basic system

  • OS: Windows (64 bit) or Mac OS X
  • CPU: Intel or AMD 64-bit processors
  • Graphics card: Nvidia or AMD graphics cards
  • System memory: 4GB
  • Display resolution: 1280 x 1024

Example high performance system(s)

  • OS: Windows 10 Pro
  • Motherboard: Asus 270-WS
  • CPU: Intel Core i7 7700K
  • Graphics card: Nvidia Geforce GTX 1080 Ti, Quadro P6000 (10-bit support), or AMD Radeon RX Vega, FirePro WX9100 (10-bit support)
  • System memory: 64 GB
  • RAID: 2x Samsung NVMe SSD 960 PRO 1TB in RAID0
  • Display: Dell UltraSharp UP2716D (10-bit support)

Note: Only matching professional-level graphics cards and displays can support 10-bit output. Refer to the FluoRender user's guide for setting 10-bit output.


1. What computer hardware is good for running FluoRender?

First of all, FluoRender is built to run on a personal computer with good graphics processing capabilities. Although most of today's personal computers can run FluoRender, including Windows desktops, laptops, Apple MacBooks, iMacs, and MacPros, it is best to purchase one with a gaming level or professional graphics card. Wikipedia provides detailed comparisons of graphics card from both Nvidia and AMD. Generally speaking, a graphics card with higher "Processing Power GFLOPs" is also better for FluoRender. We would recommend a top-of-the-line gaming graphics card over a professional graphics card. FluoRender can take advantage of some features of a professional graphics card, such as 10-bit output and better anti-aliasing. However, the difference is subtle in most situations. Second, strong CPU processing power is generally desired. We would recommend a latest CPU with higher clock frequency over more cores. Third, if you have large data sets to process, equip as much system memory as possible. For the year 2015, the consumer level computers can be equipped with as much as 64 GB of system memory, while a professional desktop can have 512 GB or more. Last, if you want to load data quickly or play back large time sequence smoothly, you need high speed access to hard drives. We would recommend a discrete RAID controller with abundant cache. Speed of hard drives is also important for handling large data sets. We would recommend 4 or more solid state drives configured in RAID0 mode.

2. Why can't I start FluoRender?

There are several possibilities for FluoRender to fail. First, check if the graphics driver is installed and updated to the latest version. Some old graphics card may not support OpenCL, which is required since version 2.15. If that is the case, you can download and try an earlier version of FluoRender. Since version 2.16, we require the graphics card to support at least OpenGL 3.3. If you have an old graphics card and want to use FluoRender on it, please replace your graphics card or download an old version of FluoRender. Second, make sure that your operating system supports 64-bit applications. Since version 2.15, we have dropped the support of 32-bit applications, which means FluoRender is 64-bit only. For Windows, you have to purchase the x64 version of the operating system; for Mac OSX, you have to update to the recent versions. Finally, FluoRender may not be properly installed, or some required modules have been accidentally uninstalled. Reinstalling FluoRender may solve the issue.

3. Why can't I load a file into FluoRender?

FluoRender can only load supported file formats, which include TIFF and some microscopy manufacturer specific formats. We write our own readers for these formats to achieve the best performance, especially for large data and time sequence data. So, we can only support "Open" and standard formats. If you have files of unsupported formats, you have to convert the format using a third-party tool. ImageJ can be a good choice in most situations.

4. Why can't I use some of the functions in FluoRender?

If you can use FluoRender for the basic visualizations of volume data, but not some advanced functions, such as paint brushes, it means your system does not support all OpenGL features. This can be that you are using a virtual machine, a remote client, or a system with an integrated graphics card with limited capabilities. You may want to upgrade your system to a standalone desktop computer with the latest graphics hardware to use all features in FluoRender.

5. Does FluoRender have a Linux version?

The official FluoRender releases only include a Windows version and a Mac OSX version, both 64-bit. If you want to run FluoRender on systems other than these, you can download the source code of FluoRender and build it on a different operating system. Additionally, you can send us emails and let us know your requirements.

6. How can I fix FluoRender crashes when rendering and computing take long time?

You may add a registry value, called "TdrLevel", on Windows. More information can be found here.

Sample Data

1. Zebrafish Head
Confocal dataset of 5 day old transgenic zebrafish larva, stained for anti-actin, anti-GFP (recognizing the isl1:gfp transgene), and ToPro3 (nuclear stain). Voxel size = 1.25 x 1.25 x 3.0 microns.

fluorender zebrafish01isl1actinCy3Top3_actin.tif [35MB]

isl1actinCy3Top3_isl1.tif [35MB]

isl1actinCy3Top3_Top3.tif [35MB]


FluoRender Mailing List


Yong Wan, Ph.D
This email address is being protected from spambots. You need JavaScript enabled to view it.
Scientific Computing and Imaging Institute, University of Utah


Chuck Hansen
Scientific Computing and Imaging Institute, University of Utah

Chi-Bin Chien (decesed)
Dept. Neurobiology & Anatomy, University of Utah


Brig Bagley, Research Software Engineer
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Hideo Otsuna, Ph.D
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Hideo Otsuna, Yong Wan, Chi-Bin Chien and Charles Hansen. "Interactive Extraction of Neural Structures with User-Guided Morphological Diffusion", Publication No. US20140104273 A1. Application No. US 14/051,947.

Yong Wan, Hideo Otsuna, Kristen Kwan and Charles Hansen. "Real-Time Dense Nucleus Selection from Confocal Data", Eurographics Workshop on Visual Computing for Biology and Medicine, 2014.

Yong Wan*, Hideo Otsuna*, Chi-Bin Chien and Charles Hansen, "Interactive Extraction of Neural Structures with User-Guided Morphological Diffusion", in Proceedings of 2012 IEEE Symposium on Biological Data Visualization (BioVis), 2012. 

Yong Wan*, A. Kelsey Lewis*, Mary Colasanto, Mark van Langeveld, Gabrielle Kardon and Charles Hansen, "A Practical Workflow for Making Anatomical Atlases in Biological Research", IEEE Computer Graphics and Applications, vol. 32, no. 5, 2012, pp. 50-60.

Yong Wan*, Hideo Otsuna*, Chi-Bin Chien and Charles Hansen, "FluoRender: An Application of 2D Image Space Methods for 3D and 4D Confocal Microscopy Data Visualization in Neurobiology Research", in Proceedings of 2012 IEEE Pacific Visualization Symposium (PacificVis), 2012, pp. 201-208.

Yong Wan*, Hideo Otsuna*, Chi-Bin Chien and Charles Hansen, "An Interactive Visualization Tool for Multi-channel Confocal Microscopy Data in Neurobiology Research", IEEE Transactions on Visualization and Computer Graphics, vol. 15, no. 6, 2009, pp. 1489-1496.

Joining the FluoRender Users Mailing List

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