Assets 6

Download the installation packages under "Assets". Choose FluoRender2.23_win64.exe for Microsoft Windows 7, 8, 8.1, and 10. Choose FluoRender2.23_mac64.pkg for Apple OS X and mac OS 10.9 and above.

FluoRender Version 2.23 added these new features:
• ImageJ and Bioformats support, an expanded file format support is available by configuring FluoRender to use ImageJ and Bioformats functions. This feature needs ImageJ and Bioformats to be preinstalled.
• Automatic rotation center anchoring for large data, users can configure a zoom ratio for the rotation center anchoring to become active. Users can also manually override the rotation center anchoring mode. The computing of the rotation center has also been improved by considering transparency and MIP mode.
• Depth attenuation linked to rotation center, the calculation of the depth attenuation effects is linked to rotation center.
• Unified OpenCL programming interface and management, we have improved the OpenCL programming interface so that all functions implemented using OpenCL kernels are managed with the same interface. Functions that use OpenCL kernels include component analysis and filtering.
• OpenGL resource management, OpenGL resources, including framebuffers, textures, vertex buffers and arrays, are managed using centralized interface. The new interface fixed previous memory leaks and improved overall performance. Graphics memory is used more efficiently for data sets with many channels or requiring enlargement.
• New color maps and color map modes, new color maps and color map modes are added. The compatibility between color maps and other volume property settings have been improved. For example, color map, shading, and MIP can all be configured simultaneously.
• Ruler profile improvements, the output of ruler profiles is reorganized for easier processing in Excel. A ?F/F option is added to the ruler profile settings.
• Command line options, a series of command line options are supported. Users can launch FluoRender, load data, and export a movie using just the command line. This may streamline the visualization of a large amount of data.
• Brush tool undo is on by default, the undo and redo operations are turned on by default. The number of operation history is set to 1 by default.

The 2.23 release of FluoRender also fixed these issues:
• Components may not be selected correctly after analysis.
• Components may be slow to select after analysis in a very large data set.
• Memory leaks.
• Render view may not be refreshed correctly.
• A duplicated volume may not be rendered correctly.
• A duplicated volume may not be removed correctly.
• Volumes of different resolutions may not be rendered correctly in the depth mode.
• Project files saved on one operating system may not be loaded on a different one.
• Clipping plane display mode was not saved correctly in project files.
• Clipping plane results may not be computed correctly for multiresolution data.
• Voxel spacing values may not be updated correctly for multiresolution data and multichannel data.
• Sampling rate may not be computed correctly for multiresolution data.
• The threshold value of the brush tool may not be set correctly.
• An ImageJ Hyperstack file with only one Z section may not be read correctly.
• A tracking result file may not be read correctly.
• Paint brush may not be used on Intel integrated GPUs with OpenGL 4.0 support.

@basisunus basisunus released this Mar 27, 2018 · 170 commits to master since this release

Assets 6

Download the installation packages under "Assets". Choose FluoRender2.22.3_win64.exe for Microsoft Windows 7, 8, 8.1, and 10. Choose FluoRender2.22.3_mac64.pkg for Apple OS X and mac OS 10.9 and above.

FluoRender Version 2.22.3 added these new features:

  1. A multiresolution data format, VVD, is supported. Extremely large data can first be saved in the VVD format and then loaded into FluoRender. The VVD format was designed by Takashi Kawase at the Janelia Research Campus, HHMI.
  2. You can use finger gestures to rotate, pan, and zoom the view on a tablet computer or Ultrabook that supports multitouch.
  3. You can paint select structures with a digital stylus using the Wacom technology, which include Wacom-branded products and tablet computers using the Wacom technology. The pressure reading of a pressure-sensitive stylus is used to control the selection strength. Additionally, the wheel on the Wacom Airbrush can be used to control the brush size.
  4. The rotation center anchor function is automatically turned on or off depending on the zoom ratio. This allows view rotation operations to be usable when zoom into the details of a very large data set.
  5. You can choose an orthographic view from a drop-down list, including +X, -X, +Y, -Y, +Z, and -Z views.
  6. A TIFF file storing data in tiles can be loaded. Extremely large data can be saved as tiled TIFF files. When the X or Y resolution of an image section exceeds 60K, ImageJ may fail to load the data.
  7. You can set a keyframe and save the angle of perspective view. You can use this feature to animate the angle of perspective angle.
  8. You can set a keyframe and save the timepoint index for a time sequence. You can use this feature to animate the play back of a time sequence.
  9. When you load a volume data set, the progress dialog also shows the current settings for large data streaming. You may decide to disable streaming if the mode is undesired but turned on from previous sessions.
  10. When the large data streaming mode is turned on, the workload can be more accurately predicted based on the settings and user interaction speed. Large data can be manipulated on low-end or old computers more easily. However, the latest computer hardware is still recommended for large data.

The 2.22.3 release of FluoRender also fixed these issues:

  1. 16-bit data were not displayed correctly when the intensity values are inverted.
  2. 16-bit multichannel TIFF files were not loaded correctly.
  3. Program crashed when the large data streaming mode was switched on after a data set had been loaded.
  4. Program failed to start on an Apple computer when the CPU was not an Intel Core i7.
  5. Channel intermixing mode is not displayed correctly when a project was loaded.
  6. Perspective view angle might not be set correctly.
  7. Failure of loading a very large ImageJ Hyperstack file, or a time sequence in ImageJ Hyperstack format was not loaded correctly
  8. Failure of loading a very large Zeiss LSM file, or a time sequence in LSM format was not loaded correctly.
  9. Generated components could not be selected correctly before a component analysis is performed.
  10. Data bricks were not loaded correctly on certain AMD graphics cards when the large data streaming was turned on.
  11. Program crashed when a full-screen render view was closed using OS functions.

Note: we have tested FluoRender on different mobile computers with an external GPU. Windows 10 on a tablet computer or Ultrabook with the Thunderbolt 3 interface is recommended. Apple computers may work depending on the combination of hardware models and OS versions.

@basisunus basisunus released this Nov 1, 2017 · 272 commits to master since this release

Assets 6

Download the installation packages from the links down below.

We are pleased to announce the 2.22 release of FluoRender. This version incorporated several new features and issue fixes. The major changes of this version include:

  1. Fixed visualization issues in the large data streaming mode.
  2. Added multichannel colocalization analysis to the component analysis dialog.
  3. Added the pin rotation center function to automatically determine the rotation center after panning.
  4. Fixed an OpenCL query issue when multiple graphics cards are present.
  5. Added a texture size limiter in the setting dialog to divide large data into bricks when large data streaming is turned off.
  6. Added color consistency function to the component analysis dialog.
  7. Improved component analysis functions for the large data streaming mode.
  8. Fixed an issue of reading texture files linked to mesh objects.
  9. Added a 4D script to export ruler profiles.
  10. Added support of ImageJ hyperstack files that are larger than 4GB.
  11. Improved reading speed for certain types of TIFF files.
  12. Fixed an issue that the output brightness adjustment is incorrect when saving an enlarged screen capture.
  13. Added new OpenCL kernels.
  14. Improved the brush selection in the large data streaming mode. Brush selection can diffuse across brick borders.
  15. Added a function to resample volume channels.
  16. Added a function to automatically resample mask volumes of mismatched resolutions.
  17. Added an option for brush size unit. A brush with the data-dependent size zooms with the render view to match 3D structure size;
  18. Improved paint brush speed in the large data streaming mode by limiting the bricks to the render view.
  19. Added successive execution of OpenCL kernels.
  20. General user interface improvements.

💡 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 👻
🍎 For Mac computers, only models from 2010 and later are supported. If your Mac computer was manufactured before 2010, please use an earlier version of FluoRender.

@basisunus basisunus released this Jun 20, 2017 · 362 commits to master since this release

Assets 6

Download the installation packages from the links down below.

We are pleased to announce the 2.21 release of FluoRender. This version incorporated several new features and issue fixes.
The new features include:

  1. Isolate volume groups. You can select a volume group from the Workspace panel and isolate its display.
  2. Component analysis for large data sets. The component analysis works when large data streaming is turned on. The ID allocation of the component generation algorithm has limited the size of a data set to 1023³. When the brick size in the streaming settings is smaller than 1024, component analysis is performed per brick. Then, all bricks are stitched.
  3. Linux support. The source code has been modified to be compatible with Linux compilers. Users need to generate the Linux executables from the source code. The Linux compatibility was made available by user Mario Emmenlauer (emmenlau). We would like to thank him for his work.
    The new version of FluoRender also fixed these issues:
  4. File format reading issues related to Prairie XML files and plain TIFF files.
  5. A screen capture could not be saved correctly when the render view was cropped and enlarged.
  6. Rulers were confused in a time-dependent sequence.
  7. 4D script settings were not saved in the defaults.
  8. Paint brush results became corrupted when recent nVidia graphics drivers were used.
  9. Crash on Mac OS when IDs were assigned to selected components.
  10. In a cell tracking workflow, a component with a new ID was not linked to existing components in the automatic tracking refinement calculations.
  11. We added the choice of yellow, magenta, cyan, and orange to the default channel color settings.
  12. An issue that the render view kept refreshing when component colors were turned on in the streaming mode.
  13. Other minor issues of the user interface.

💡 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 👻
🍎 For Mac computers, only models from 2010 and later are supported. If your Mac computer was manufactured before 2010, please use an earlier version of FluoRender.

@basisunus basisunus released this Dec 19, 2016 · 423 commits to master since this release

Assets 6

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 👻.

@basisunus basisunus released this Oct 13, 2016 · 448 commits to master since this release

Assets 7

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.

@brigb123 brigb123 released this Jul 29, 2016 · 538 commits to master since this release

Assets 7

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.

@brigb123 brigb123 released this Apr 20, 2016 · 612 commits to master since this release

Assets 8

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.

@brigb123 brigb123 released this Oct 30, 2015 · 702 commits to master since this release

Assets 6

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.

@brigb123 brigb123 released this Aug 27, 2015 · 792 commits to master since this release

Assets 8

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.