v2.30

Thank you for using FluoRender. Download the installer package for your operating system from the list of assets below. Videos demonstrating the latest functions of FluoRender can be found on YouTube.

FluoRender Version 2.30 improved the user interface and added new functions. The highlights include:

• A new slider widget with dual thumbs for setting both low and high values, such as for thresholds and clipping planes. The two values can be linked for synchronized slider moving.
• The new slider can be linked to a render view and changed by the mouse wheel scroll.
• Undo and redo operations for individual parameter settings.
• Undo and redo operations for most visualization settings.
• Multi-function buttons for most visualization settings. The function of the button can be configured in the settings.
• Tabs for property settings. For example, multiple tabs can be opened for the settings of more than one volume channel. The tabs can be reorganized to be shown side-by-side.
• Tabs for most of the main user interface panels. Less often used panels can be hidden by tabs.
• New playback controls in the movie-making panel. The functions of each button or text input are explained by the pop-up tips when the mouse cursor is on top of a control.
• New templates for quickly making commonly used keyframe animations. Keyframe animations for camera movements and time sequence control are added. Making keyframe animations with just a single button click.
• Settings for the scalebar location when image crop is enabled.
• The crop frame can be modified by direct dragging in a render view.
• A new display setting tab in the main settings. New settings include a ratio for stereo rendering and a display ID for full-screen rendering.
• Support of high-resolution displays and scaling.
• The user interface layout is saved and set to the previously used settings. The layout can be reset from the main menu.

FluoRender 2.29.3 Released

Thank you for using FluoRender. Download the installer package for your operating system from the list of assets down below. Videos demonstrating the latest functions of FluoRender can be found on YouTube.

FluoRender Version 2.29.3 improved usability and fixed issues in the previous versions.

• A new script is added to FluoRender to reconstruct a 3D scene from rulers generated by tracking feature points in a pair of stereo videos.
• New functions for saving and managing project files improve usability.
• The Magnet function is added to the Edit tool for moving ruler points.
• A new script is added for generating synthetic walk animation from an average walk cycle, which can be extracted using the ruler tracking functions.
• A new script is added for converting the components in a time-dependent data set to animated rulers, which can then be processed using the scripts for rulers.

FluoRender 2.29.3 fixed these issues:

• An issue that the total number of training frames for DeepLabCut was limited to 128.
• An issue that the current time point was not loaded from a project file.
• An issue that previous movie frames were not cleared before rendering a next frame when large data streaming was on and rendering order was set to front to back.
• An issue in reading czi file that the volume was shifted.
• An issue that FluoRender crashed when editing component ID.
• Various user interface issues

FluoRender 2.29.2 Released

Thank you for using FluoRender. Download the installer package for your operating system from the list of assets down below. Videos demonstrating the latest functions of FluoRender can be found on YouTube.

FluoRender 2.29.2 adds support to run third-party or custom Python scripts. Specifically, the DeepLabCut is integrated into FluoRender, which is typically used for analyzing animal postures from video files. Typical machine-learning operations including model training and application can be accomplished only from FluoRender's user interface without direct interactions with Python.

• A new script for markerless training of video files. Use FluoRender's ruler tools to place points to be tracked on frames of a video file. Run the script to launch training using the DeepLabCut. Both Python and DeepLabCut need to be installed correctly by user.
• A new script for analyzing animal postures from video files. This script applies the trained model from the DeepLabCut and generate rulers, which can then be analyzed using existing scripts for ruler information extraction.
• Nikon ND2 format is supported on macOS.
• A smoothing setting is added to the script for image registration. It filters the motion vectors of registered results to make typical drift movement smooth.
• Volume properties can be automatically generated at loading by machine learning. The Auto Apply setting can be switched on in the Machine Learning Manager.
• A new script for analyzing the fluorescent intensity change over time on segmented components.

FluoRender 2.29.2 fixed these issues:

• The script for image registration failed to generate results when data had low signal-to-noise ratio.
• Laser wavelength and color information was not read correctly from the Bruker/Prairie View format.

FluoRender 2.29.1 Released

Thank you for using FluoRender. Download the installer package for your operating system from the list of assets down below. Videos demonstrating the latest functions of FluoRender can be found on YouTube.

FluoRender 2.29.1 included several improvements over the measurement functions and fixed issues. Additionally, the code directories and CMake file were reorganized to enable building on Linux systems. An executable file built on Ubuntu 22.04 is provided for download. This is an experimental build for Linux. We can make improvements per user request. Please provide detailed information on your OS version and hardware configuration when contacting us. Furthermore, a brief instruction for building on Linux systems is provided. Note that hardware support of OpenGL and OpenCL is needed in order to run FluoRender. Make sure that a specific Linux distribution and hardware configuration can support GPU computing. Please reference the readme file or use manual for further information.

• The ellipse ruler can be used as an ROI to sample intensity values of volume data. The region is defined by the projection of the ellipse from the viewing angle.
• We added a script to compute the fluorescence intensity changes. The changes are computed based on the resting state of an ROI, which in turn is estimated from the background intensity levels.
• We provide three methods of interpolation for ruler points: step, linear, and smooth.

FluoRender 2.29.1 fixed this issue:

• An issue that intensity values were not sampled correctly by rulers.

FluoRender 2.29 Released

Thank you for using FluoRender. Download the installer package for your operating system from the list of assets down below. Videos demonstrating the latest functions of FluoRender can be found on YouTube.
FluoRender Version 2.29 added a machine-learning module for training and applying various settings in FluoRender. The current version implemented machine learning for localized component generation (for volume segmentation) and volume property settings (for visualization). We also improved the ruler tools to enable measurement over time. Combined with the ability to directly load video files, the improved ruler tools can be used for analyzing movements and gestures in videos. Several issues in previous versions were also fixed.

• A unified user interface, called the machine learning manager, is added for the management of all machine-learning related operations. These operations are organized into categories, each having a similar workflow to manage training tables and start/stop training.
• Machine learning results can be applied to generate components at local level for more accurate and easier volume segmentation.
• Machine learning results can be applied to generate volume property settings.
• The locations of ruler points can be modified over time. Rulers can be animated over time to track the movements of single points or complex behaviors.
• A Magnet tool allows drawing a 3D curve and attracting closest ruler points to the curve. Rulers with multiple points can be modified easily with the magnet tool, especially for tracking over time.
• A Redraw tool allows drawing a 3D curve and redistributing all points of the closest ruler on the curve. Rulers with multiple points can be redrawn quickly without changing their topology.
• A setting is added to adjust the distance between two ruler points in the screen space when the pencil tool or magnet tool is used for drawing a curve.
• A script task for exporting ruler coordinates over time. Rulers can be used to track complex movements over time. Use this script to export the analysis results.
• A script task for replacing a volume channel. Use this script to change volume data upon finishing and rewinding of a script.
• A script task for switching the current script. Use this script to load a new script upon finishing and rewinding of a script.
• A script task for loading a project. Use this script to load a project upon finishing and rewinding of a script.
• Image registration can now be constrained using a paint mask. Only the data within the mask are considered, which can improve efficiency and accuracy.
• A DPI setting is added to the screen capture options. It can be used to automatically enlarge the captured image when a high DPI value is set. A base value of 72DPI is used. The DPI value is also saved in TIFF metadata.
• Commonly used video files can be directly loaded into FluoRender as 3-channel time-dependent volumes of single Z slices. Supported video containers include MP4, M4V, MOV, AVI, WMV, etc.
• When loading TIFF images of the 32-bit floating point format, the intensity values are converted to 16-bit integers.

FluoRender Version 2.29 made these improvements or fixed issues:

• An option to customize the behavior of the fixation operation in component generation. It determines whether the fixated regions can continue growing into other regions or they need to be constrained.
• A memory allocation issue when a time-dependent data set was processed using scripts.
• An issue that FluoRender crashed when an external program, such as a web browser or spreadsheet editor, was called to display analysis results using a script.
• Other user interface issues.

Notes:

• The Windows installer was updated on Jan-17-2023 to grant access permissions to the machine-learning tables in the installed directory. This is necessary for the machine-learning module to work. Otherwise, copy the FluoRender folder to a user directory.

FluoRender 2.28 Released

Thank you for using FluoRender. Download the installer package for your operating system from the list of assets down below. Videos demonstrating the latest functions of FluoRender can be found on the channel "FluoRender One" on YouTube.
FluoRender Version 2.28 added useful and practical functions for typical workflows to analyze fluorescence images. Several issues in previous versions were also fixed.

• The keyframe animation system supports setting keyframes on the sequence numbers of time-dependent data.
• The primary color of a volume channel is included in a keyframe. The animation of the volume color provides a visual indicator for the time progression.
• Improvements to the performance and robustness of the tracking of brush-selected data.
• A new script for rigid-body registration of images in a time sequence. The registration results can be saved as a new sequence and/or directly applied to render view transformations for real-time analysis.
• Fluorescence intensity sampling with the ruler tools. Intensity values are interactively updated.
• A ΔF/F mode that automatically computes the background intensity and normalizes fluorescence intensity values.
• Real-time fluorescence intensity sampling on registered time sequence data with the ruler tools.
• New analysis result templates supporting offline viewing.
• The ridgeline template supports line colors from ID values.
• Width adjustment to the borders of clipping planes.
• A new clipping plane display mode to show borders of only front facing clipping planes.
• New settings to the ruler profile script provide the maximum intensity and its location along a ruler.

FluoRender Version 2.28 fixed these issues:

• OpenCL code stability and performance issues on various platforms.
• A render view scaling issue on macOS computers.
• An issue that the default browser failed to launch when a script with analysis results was executed on macOS computers.
• An issue that the component generation did not produce valid results when both distance field and density field were enabled.
• An issue that the paint brush operation crashed FluoRender on macOS computers.
• An issue that the paint brush position did not match the render view on macOS computers.
• Flicker of UI widgets when a keyframe animation was played on Windows computers.
• An issue that exported Tiff volumes were not readable by programs such as Photoshop.

FluoRender 2.27 Released

Thank you for using FluoRender. Download the installer package for your operating system from the list of assets down below.
FluoRender Version 2.27 made substantial changes to the script system for automated analyses of time-dependent data. It also improved the OpenCL kernel system. Several issues in previous versions were also fixed.

• Improved connectivity of the Grow Ruler tool. The default size threshold for the Grow Ruler is lowered to make connections on very thin structures. It is useful when the Grow Ruler is used together with a thinning filter to first extract the skeletal structures and make measurements.
• Track map clear function. A button is added to the Tracking window to clear an existing track map.
• Linear interpolation for volume cropping and resizing. An option for interpolation method is added to the saving volume dialog.
• Frame settings for basic rotation movie export. Frame range, movie time, and FPS can be set for basic rotation movies, which allows finer control of the playback.
• Component display mode. An option is added to the volume property settings to control whether components are displayed using distinctive colors. The association of the component display and script running is therefore removed.
• Component ID edit. An option is added to the volume property settings to control whether components are displayed using distinctive colors. The association of the component display and script running is therefore removed.
• 16-bit data support for OpenCL kernels. The result from applying an OpenCL kernel remains at 16 bits when the input channel is 16 bits. Several preprocessor definitions are added to the OpenCL kernel code to make sure data bit depth is automatically and correctly selected.
• An OpenCL kernel to remove background. The new OpenCL kernel code can be used to remove background signals that obscure major structures. The background is separated from structures through the computing of local intensity distributions.
• Applying script in a batch process. A script can be applied to independent data sets in a batch process in addition to a time sequence. Put files need processing in the same folder and enable batch process. The files are treated as if they were time point data in a time sequence. Single file being considered as one time point can also be processed.
• A new time mask to control script running. A time mask that uses a bitmask scheme to control how a script command is executed relative to the time code and data loading.
• Macro command in script. The script command generate_comp can receive the file name of a macro command as a parameter and use it for component generation. Use the component window to determine appropriate settings for component generation and save it as a macro command. Then, the command can be applied to a time sequence.
• A script to track labeled masks. A script command with the type mask_tracking is added. It tracks structures labeled by masks over time. Structures are tracked based on spatial adjacency and similarity of intensity values.
• A script to clear masks. A script command with the type clear_mask is added. It resets all msk and lbl files to zero values.
• A script to compute the background intensity level. Similar to the script command to remove background, a script command with the type backg_stat is added to extract the background and compute the statistical information on its intensity levels.
• A script to export analysis results with infographics in html format. A script command with the type export_analysis is added to export analysis results in html format. The html file is generated based on templates. The template html files leverage Javascript and the D3 library to present tabular information as infographics.
• A script for fully automated analysis. A script file comps_gen_track_analyze.txt is added to perform fully automated analysis. It generates components in the first time point of a sequence, filters the components based on size, tracks the components over time, and presents the intensity changes over time in a ridgeline graph.
• An html template to present component analysis results in a spreadsheet. An html template called table.html is added to present the tabular information from component analysis in a spreadsheet.
• An html template to present component analysis results in ridgeline graphs. An html template called ridgeline.html is added to present values from component analysis using ridgeline graphs.

FluoRender Version 2.27 fixed these issues:

• An issue that the ID of a ruler was not saved correctly in a project file.
• An issue that the Prairie-Bruker xml formal was not read correctly when information on the Z section size was not available.
• An issue that newly assigned IDs for components were not saved correctly in the label file.
• An issue that the generation of consistent colors over time for tracked components was not working correctly.
• An issue that a file with a long file name, including its path, was not saved correctly on Windows.
• An issue that the rendering sample rate became too low for unusually anisotropic data.
• An issue that an OpenCL kernel was not freed properly after use.
• An issue that a cropped volume was not saved correctly when its clipping planes were rotated.
• An issue that copying a channel as mask into another channel did not work correctly.
• An issue that volume resizing and cropping did not work at the same time.
• An issue that a mask file over 2 GB could not be read correctly.
• An issue that component kept growing after the application of fixation.
• An issue that a value of discrete states was not saved correctly in a project file for key-frame animation.
• An issue that the frame number was updated correctly when a range was selected for a time sequence.
• An issue that play time and FPS values were not updated correctly when one of them or the frame range were changed.
• An issue that the numerical values in a file name for Z sections, channels, and time were not correctly interpreted at the same time.
• An issue that the frame number was not counted correctly when running a script.
• An issue that certain types of T series and Z series Prairie-Bruker files were not recognized correctly.
• An issue that the background signals near image boarder was incorrectly identified as components when the density field feature was enabled.
• Various user interface updates and improvements.

FluoRender 2.26.3 Released

Thank you for using FluoRender. Download the installer package for your operating system from the list of assets down below.
FluoRender Version 2.26.3 added several data visualization and analysis features that users may find useful in practice. Several issues in previous versions were also fixed.

The new features in the 2.26.3 release of FluoRender include:

• Enhanced ruler group functions. Multiple rulers can be selected from the ruler list and have their group ID and color changed. The rulers in a group can be selected together with their group ID. The selected rulers can be hidden or shown together.
• Camera target lock in key-frame animations. The target of the render view can be locked on an object while the movement of the camera still follows existing key frames.
• Volume cropping. An option is provided to save a cropped volume channel. The cropping is determined by the clipping planes. The cropped volume can be rotated or reoriented by rotating the clipping planes.
• Support of reading tiled LIF files. FluoRender will read the tile positions from the metadata and assemble the tiles into a full scan.
• Support of reading tiled CZI files. FluoRender will read the tile positions from the metadata and assemble the tiles into a full scan.

FluoRender Version 2.26.3 fixed these issues:

• An issue that components could not be highlighted in the render view.
• Improved component fixation.
• Several issues that may cause component generation to crash or fail.
• Key-frame inbetween values changed when key frames were reordered.
• Scale bar text was not aligned.
• An issue that the grow ruler could only compute the result for one time before restarting or reloading the data.

FluoRender 2.26.2 Released

Thank you for using FluoRender. Download the installer package for your operating system (Windows or macOS) from the list of assets down below.
FluoRender Version 2.26.2 strengthened data analysis in the large data streaming mode, which divides a large data set into multiple data bricks. Changes made to the paint brush and component analyzer allowed data skipping of unselected bricks to improve computing speed when only local features of a large data set are being analyzed.

The new features in the 2.26.2 release of FluoRender include:

• Multichannel support in component distance calculation. A unified adjacency matrix is computed for an arbitrary number of channels. Each channel needs to be segmented and analyzed using the component analyzer. Then the mutual distances of the components are computed as the elements of the adjacency matrix.
• Upscaling movie export. An exported movie, in QuickTime or Tiff format, can be upscaled to higher resolutions.
• Ruler group. Rulers created in the Measurement window can be assigned with a group number.
• Component length. The length of each component is calculated in the component analysis. The length is computed as the length of the longest axis using the Principal Component Analysis.
• Brick skipping in component analysis. When the large data streaming is enabled and use selection mask is checked, the component analysis functions ignore data bricks that are not selected by a mask. Therefore, the computing time for a local structure within a large data set is significantly reduced.
• Brick skipping in brush painting. When the large data streaming is enabled, bricks not covered by a brush stroke are not included in the computations. Therefore, the computing time for selecting a local structure within a large data set is significantly reduced.

FluoRender Version 2.26.2 fixed these issues:

• Removed a limitation to Tiff file name length.
• The intensity values of 8-bit Leica files were not scaled correctly.
• The color lookup tables in Leica files were not applied correctly.
• Zoom level display mode was not read correctly from a project file.
• A file sequence was not loaded correctly on Mac OS.
• An ellipse ruler was not computed correctly when its ruler points were moved.
• Component size was not computed correctly for a single image section in the streaming mode.
• A single component spanning multiple bricks may not be combined correctly.
• Component colors were not displayed correctly when Alpha is turned off in the volume settings.
• A single component spanning multiple bricks may not be assigned with a matching color for all its parts.
• Components were not selected correctly in the streaming mode.

FluoRender v2.26 Released

Thank you for using FluoRender. Download the installer package for your operating system (Windows or macOS) from the list of assets down below.
FluoRender Version 2.26 added support of reading several microscopy formats natively as well as other features. Many users contributed to this release by providing design concepts, function tests, and bug reports. We would like to thank every user, who help make FluoRender a better tool.
Notice that we wrote our own code for reading most of the raw microscopy formats. Not all format possibilities have been tested. If you experience any issue opening a file, please contact us by providing a sample file.
The new features in the 2.26 release of FluoRender include:

• Zeiss ZISRAW CZI file support. The implementation of the CZI file reader in FluoRender version 2.26 is based on the ZISRAW file format design specification V 1.2.2, published in July 2016.
• Nikon ND2 file support. The implementation of the ND2 reader in FluoRender version 2.26 is based on the ND2 SDK version 1.1.0.0. The SDK only provides support on Windows and Linux. Therefore, the ND2 file support is not available on macOS.
• Leica LIF file support. The implementation of the LIF file reader in FluoRender version 2.26 is based on the Leica Image File Formats Version 3.2, published in September 2016. A LIF file may contain multiple images from different experiments. Use the new series selection function to select one image at loading.
• Leica LOF file support. The implementation of the LOF file reader in FluoRender version 2.26 is based on the Leica Image File Formats Version 3.2, published in September 2016. A LOF file can only contain one image.
• Ruler prune tool. Ruler prune tool deletes very short branches on an automatically generated ruler using the grow ruler tool.
• New zoom ratio display modes. There are now three zoom ratio display modes: view-based, pixel-based, and data-based. The data-based mode maps the physical size of a volume channel to screen pixels. A scale bar of the same length across several sample files can be guaranteed in the data-based mode.
• Updated batch reading. The batch reading mode is separated from 4D sequence reading. For example, a LIF file contains multiple images, each being a 4D sequence. Check the batch mode to switch between images. Check the 4D sequence mode to enable 4D play back for the current image.
• OpenCL device selection. On a system with multiple GPUs, use the OpenCL device selector to determine the GPU for OpenCL processing.

FluoRender Version 2.26 also fixed these issues:

• Components cannot be updated correctly after an existing result.
• Grow selection and grow ruler may not work properly for small-size data.
• Crash when deleting rulers.
• Interaction speed decreased significantly at high magnification ratio on a high-resolution display.