FluoRender 2.20.1

Download the installation packages from the links down below.

The version 2.20.1 of FluoRender adds OpenGL benchmark features. Use the command line batch files (for Windows) or shell script command files (for Mac OS) to test a system's rendering speed.
Watch this video tutorial for more details: https://youtu.be/ggOLCX1fBs0
It also includes the following improvements:

1. Fixed a render view update issue when the front-to-back compositing is used.
2. Fixed an issue that prevents a TIFF sequence with suffix ".tiff" to be loaded.
3. Added an iteration number setting for clustering.
4. Fixed an issue that render view is not immediately updated after loading files.
5. Fixed an issue that large data are not loaded correctly on AMD FirePro graphics cards.
6. Fixed an issue that FPS calculation is not correct on Mac OS.
7. Fixed an issue that may cause crash when exiting the full screen mode.
8. Added the full screen mode for Mac OS.
9. Fixed an issue that may cause the renderings to become blurry when zoomed in, even if data smoothing is turned off.
10. Included benchmark files in the data directory. One grid image file can be used to test rendering resolution for large data. The 3-channel zebrafish data can be used for speed testing. Use the command line options for speed testing.
11. Fixed an issue of reading ImageJ hyperstack TIFF files. When a time sequence only contains one Z section at each time point, reading may cause FluoRender to crash or load incorrect results.
12. Fixed an issue of incorrect maximum value when reading large 16-bit TIFF files.
13. Fixed an issue of reading more than one TIFF Z sequence from one directory.
14. Added association to the FluoRender project files for Windows.

💡 Note: make sure your graphics driver is updated on Windows systems. Outdated graphics drivers may prevent the program from using the latest OpenCL functions, resulting in a dynamic link library error 👻.

FluoRender 2.20

We are excited to announce the latest release of FluoRender, version 2.20, which incorporates improvements, bug fixes, and new features.
See how FluoRender works on YouTube:
https://www.youtube.com/user/basisunus/videos?sort=dd&shelf_id=0&view=0

The changes include:

1. Fixed an issue that changed render view zoom factor when setting key frames.
2. Added three clustering algorithms for segmentation: expectation-maximization, DBSCAN, and k-means. Users can use these methods in the "Component" window. They were also integrated into the tracking algorithms to automatically segment components when tracking is executed.
3. Improved tracking accuracy. Users can also set a series of parameters in the "Tracking" window to fine tune the behavior of the tracking.
4. Fixed an issue of reading Prairie/Bruker xml formats, when the TIFF files are saved/processed by third-party tools.
5. Added a new 4D script for tracking sparse particles.
6. Fixed an issue that paint brush was not working properly on the latest AMD graphics cards.
7. Fixed an issue that component generation failed on the latest AMD graphics cards.
8. Added a density parameter to the basic settings of component generation. Use this parameter to better separate cells/nuclei.
9. Fixed an issue that certain volume property settings became unavailable when switching between MIP and normal render modes.
10. Fixed and issue that render view became blank or corrupted on OS X Yosemite.
11. Added render view capture enlargement. Users can capture and save an image larger than the size of render view.
12. Added a list of built-in 4D scripts. Users can easily select and switch 4D scripts without browsing to the actual files.
13. Other minor user interface improvements.

Note: download FluoRender_2.20_mac64.pkg for macOS Sierra or FluoRender_2.20_osx64.pkg for earlier versions OS Xs.
Note: make sure your graphics driver is updated on Windows systems. Outdated graphics drivers may prevent the program from using the latest OpenCL functions, resulting in a dynamic link library error.

FluoRender 2.19.4

We are excited to announce the latest release of FluoRender, version 2.19.4, which incorporates improvements, bug fixes, and new features.

In this release, we mainly improved the usability of a series of functions for 4D analysis, including the component analyzer, 4D scripts, paint brush tools, and format supports. We have also made a series of video tutorials and published them on YouTube:
https://www.youtube.com/playlist?list=PLSBz7un7RyZhO51UWhmGiusaJebmaWPbc

The details of the improvements are:

1. We reorganized the 4D script settings. The user interface has been moved from the setting window to the movie export panel as a tab. 4D scripts allow customization of the time sequence play back in FluoRender. 4D data can be processed and analyzed with a series of scripts, examples of which can be found in FluoRender's installation directory. For more intuitive 4D tracking and analysis, we also added a series of new 4D scripts.
2. We added a size limiter to the basic operations of the component analyzer. Component generation can also be applied to currently selected structures.
3. Different paint brush tools (select, diffuse, un-select, etc.) can remember their own size settings. This allows more intuitive switching among brush tools.
4. We added a new calculation operation for combining any number of channels into RGB.
5. We improved OpenGL performance on certain platforms by removing query functions from render loops.
6. We added ImageJ hyperstack TIFF support. Convert an unsupported format by FluoRender to hyperstack, which supports both time sequence data and multichannel data.
7. We improved the processing of 16-bit data.
8. We added a mask saving function for all data formats. For example, you can paint select and perform component analysis on an ImageJ hyperstack (or Olympus, Zeiss, Prairie, etc. formats) and save the results with masks.
9. We improved the user interface. For example, control widgets in the property panel are only enabled when the corresponding function is enabled.
10. We have made a series of tutorial videos and published them on YouTube. These videos cover FluoRender's functions from the basic operations to advanced features such as 4D tracking. You can find these videos by searching "fluorender" at YouTube.com.

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.

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.

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.

Installation

- 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.

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.

Installation

- 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.

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.

FluoRender 2.15.3

We are pleased to announce the release of the version 2.15.3 of FluoRender.
This version fixed several issues from previous releases, most of which were
related to the large data streaming mode.

These issues were fixed:

1. Exporting movies with the large data streaming on may write incomplete
   results;
2. View port capturing and key frame animations may stop working with the
   large data streaming on;
3. Incorrect effect rendering (shading and/or shadowing) may occur with the
   large data streaming on;
4. Multiple channels may be rendered incorrectly with the large data streaming
   on;
5. Paint-selected masks may be rendered incorrectly with the large data
   streaming on;
6. Large data may be clipped at high zoom ratios.

Additionally, we included a new feature in this version:

1. It now allows users to select one GPU for dedicated OpenCL calculations
   when multiple OpenCL-capable GPUs are installed and activated in the system.
   GPU selection is done by typing its ID in the FluoRender setting file.

Please see FluoRender's online manual and tutorials for more details.

We would like to thank Dr. Bindokas from the University of Chicago, who
pointed out most of the issues listed above and helped us test the new
versions. We appreciate any issue report and suggestion from the users. Please
take our online survey, which can be downloaded at the same website as
FluoRender (www.fluorender.org).

Thanks for your continued support of FluoRender!

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.

For more details and instructions on using FluoRender, please go to our
website at www.fluorender.org. You can also find demonstration videos on
YouTube or Vimeo.

FluoRender 2.15.1

• Minor bug fixes
• New automated key generation for advanced movie making
• Fixed a bug with MOV output
• 10 output option available for compatible graphics hardware
• Anti-aliasing option added
• Automatic cropping in movie/image output generation