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Releases: SCIInstitute/fluorender

FluoRender 2.28 Released

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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

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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

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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

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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

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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.

FluoRender v2.25.2 Released

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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 2.25.2 emphasizes on intuitive and interactive analysis on branching 3D structures, such as neuron axons, nerves, and blood vessels. Tracing these structures are automated with the Grow selection tool and Grow ruler tool. 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.
The new features in the 2.25 release of FluoRender include:

  • Grow selection supports large data streaming
    The grow selection tool allows automated identification of complex branching structures by clicking at one point. It can be applied to large data with multiple bricks. Selection mask can cross brick borders.
  • Performance improvement of the grow selection tool
    The selection speed with the grow tool is increased.
  • Threshold adjustment after brush painting
    The threshold value in the paint brush window can be adjusted after selection, on condition that the 3D viewing direction is not changed.
  • Growth direction of the grow selection can be controlled
    Click and drag the mouse to the direction of growth.
  • Pencil ruler tool
    Click and drag the mouse to create a ruler.
  • Grow ruler tool to automatically create rulers
    The grow ruler tool uses the same interactions as the grow selection tool and automatically computes rulers for branching structures. The grow ruler tool also supports large data streaming.
  • Ruler relaxation options
    Ruler relaxation can be computed using a series of constraints. Use volume data, selection mask, or analyzed components to constraint a ruler to follow 3D structures.
  • Automatic ruler relaxation
    Rulers can be relaxed immediately after drawing.
  • Ruler point deletion
    Excessive ruler points can be deleted.
  • Delete multiple rulers
    More than one ruler can be selected and deleted.
  • Ruler relaxation options
    Ruler relaxation can be computed using a series of constraints. Use volume data, selection mask, or analyzed components to constraint a ruler to follow 3D structures.
  • Render view alignment to volume selection supports large data streaming
    Render view alignment to volume selection works when there are multiple bricks.
  • OpenCL kernel for thinning/skeletonization
    Thinning/skeletonization of volume data can be computed using the thinning OpenCL kernel.
  • Updated tutorials
    We updated the tutorials to cover the latest analysis functions. See the tutorial document for more details.
    FluoRender Version 2.25.2 also fixed these issues in previous versions:
  • Render view rotation by mouse was not computed correctly when the 45 degree lock was turned on.
  • Certain channels in a saved project were not loaded.
  • Ruler information was not updated after relaxation.
  • Some UI text on Mac OS was cut.
  • A large 4D data set stopped playing after several frames when the large data streaming mode was on.
  • Certain channels were dropped in a movie output when the large data streaming mode was on.
  • Error on loading multichannel 4D data over 4 GB saved with ImageJ hyperstack.

FluoRender v2.25 Released

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Thank you for using FluoRender. Download the installer package for your operating system (Windows or macOS) from the list of assets down below.

We have strengthened the data analysis capabilities in the 2.25 release of FluoRender. Many of these features are co-developed with FluoRender users in their research. We would like to thank those users who have been working with us to make FluoRender better.

The new features in the 2.25 release of FluoRender include:

  • Ruler relaxation
    The ruler relaxation tool changes the shape of a ruler so that it becomes more relaxed. When analyzed components are present, rule relaxation also makes ruler points attracted to component centers. The inverse square law is used to compute attraction forces. When the forces reach a balance, a multipoint ruler can be used to find the centerline of the analyzed components. See Chapter 16 for more details.
  • Component projection on ruler
    The component projection tool projects analyzed components on a ruler. Use the tool to determine the distribution of components along a ruler. When a multipoint ruler is used to determine the centerline of the analyzed components, it essentially straightens the components. See Chapter 16 for more details.
  • Move ruler tool
    The move ruler tool allows moving all ruler points of a ruler together. See Chapter 16 for more details.
  • Grow selection tool
    A grow selection tool is added to the paint brush window. Use the tool to click on a structure in render view to grow selection mask from the clicked point. Hold the mouse button to continuously grow the selection mask. The grow selection tool can be used to determine all connected structures from a single point. See Chapter 15 for more details.
  • Branching ruler
    The multipoint ruler can now support branches. To create a branch, click on an existing ruler point. The total number of branches of a ruler is counted and listed. See Chapter 16 for more details.
  • Physical sizes are computed for components
    When components are analyzed, their physical sizes, computed from voxel sizes, are listed along with other values. See Chapter 17 for more details.
  • Zero rotation set
    Any rotation angles can be set as the neutral orientation. Use this tool to level tilted scans. See Chapter 7 for more details.
  • Align render view rotations to ruler
    The render view can be automatically rotated to align one axis to a two-point ruler. Or, three axes can be computed from a series ruler points using the principle component analysis. Then, the render view can be rotated to align its XYZ axes to the eigenvectors. See Chapter 16 for more details.
  • Align render view rotations to selection mask
    The principle component analysis can be performed on the voxel coordinates of a selection mask. Then, the render view can be rotated to align its XYZ axes to the eigenvectors. See Chapter 15 for more details.
  • Align render view rotations to components
    The principle component analysis can be performed on the centroids of analyzed components. Then, the render view can be rotated to align its XYZ axes to the eigenvectors. See Chapter 17 for more details.
  • OpenGL version feedback
    The specified OpenGL version in the setting file may not be used by the system. The actually used version number is written back to the setting file after launch and shut down FluoRrender once. Use this feature to diagnose OpenGL version issues. See Chapter 22 for more details.

FluoRender Version 2.25 also fixed these issues in previous versions:

  • Some spin controls failed to set the values correctly when they were input using the text box.
  • Program was constantly consuming CPU time even without any interactions.
  • Components were not rendered correctly on macOS.
  • There are also minor user interface adjustments and improvements.

FluoRender v2.24.2 Released

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Thank you for using FluoRender. Download the installer package for your operating system (Windows or macOS) from the list of assets down below.

We have made some exciting new features and improvements in the 2.24.2 release of FluoRender. Most of these features are results from user feedback and suggestions. We would like to thank those users who have been working with us to make FluoRender better.

The new features in the 2.24.2 release of FluoRender include:

  • Stereo rendering and SteamVR/Windows MR headset support. Depending on the configuration of a Windows computer, FluoRender can run in either stereo only or VR mode. When SteamVR is installed and a compatible VR headset is connected to a Windows 10 computer, FluoRender runs in the VR mode, where data sets can be viewed using the VR headset. Otherwise, FluoRender runs in stereo only mode. Stereo movies can be captured in the stereo mode and viewed on a VR-capable computer.
  • Xbox controller support. Use an Xbox controller for render view interactions. This can be useful when using a VR headset.
  • TIFF sequence file name matching supports both channels and Z sections. File names of a TIFF sequence can contain digits for both channels and Z sections. When both are present, the order of the digits can be configured.
  • A redesigned colocalization analysis user interface. The Colocalization window has been redesigned to handle multiple channels. It allows analysis to be performed only on freehand-selected structures. Analysis results are instantly shown after freehand painting or parameter change. Multiple methods for computing channel overlapping are added. A proper table widget is used to display the results with choice of color maps.
  • Mask copy and paste among channels. Mask generated for one channel can be copied and pasted into another channel. Calculations can be performed on two masks from different channels to generate a new mask. Original data of one channel can be copied as a mask as well.
  • Change inner brush stroke size by holding down the Ctrl key. You can hold down the Ctrl key and use the mouse wheel to change the inner brush stroke size.
  • Performance improvement for all real-time parameter changes using sliders. We have improved the performance of sliders, which is useful when the Auto Update feature is enabled in several analysis functions, including those in the Component Analyzer and Colocalization window.
  • Components can be more easily selected. We have made significant improvements to the Component Analyzer window. Once generated and analyzed, components can be selected and highlighted from both the component table and the render view. This allows filtering components to be more interactive and intuitive.

FluoRender Version 2.24.2 also fixed these issues in Version 2.24:

  • For 16-bit data, the erased or extracted channels became over-saturated.
  • Default 2D adjustment settings were applied to the view as well as volume groups, essentially multiplied the effects.
  • Rendering was incorrect when streaming was enabled, and multiple channels contained both masks and labels.
  • Paint brush was unable to select structures when its threshold was set to 0.0, and the option Visible Only was on.
  • Buttons and text inputs became unresponsive under certain circumstances.
  • There are also minor user interface adjustments and improvements.

FluoRender v2.24 Released

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Thank you for using FluoRender. Download the installer package for your operating system (Windows or macOS) from the list of assets.

We have made many exciting new features and improvements in the 2.24 release of FluoRender. Most of these features are results from user feedback and suggestions. We would like to thank those users who have been working with us to make FluoRender better.

The new features in the 2.24 release of FluoRender include:

  • HDR10 support. Currently HDR rendering is only supported for nVidia graphics cards on Windows 10. The HDR rendering is enabled by setting the output bits to 16 for all RGBA channels in the FluoRender setting file. If it is enabled on a system without the required hardware, settings will be automatically reset after restarting FluoRender.
  • Capture of floating-point (32 bits per channel) images. We added an option in the capture settings to allow floating-point output. The captured image will be saved with TIFF. It is useful when HDR renderings need to be presented on non-HDR displays.
  • In the tracking dialog, an arbitrary cluster number can be set for segmentation. Previously, the segmentation in tracking only separated a selection into two components. The cluster number setting allows more flexibility.
  • In the tracking dialog, segmented components using the clustering methods are automatically linked with other components.
  • Improved uncertainty filtering of tracking results. The uncertainty filter is applied for both preceding and succeeding time points. The high limit of uncertainty filtering has been removed.
  • Line thickness can be adjusted. In the settings dialog, we added a setting to adjust the line thickness, which is applied to rulers, tracks, etc.
  • Mask (*.msk) and label (*.lbl) files generated from paint selection or component generation can be loaded as volume data into FluoRender.
  • Color consistency option for tracking. An option that allows tracked components over time to be assigned with the same color is added in the tracking dialog.
  • An option to compute the volume size of a paint selected region. A use can retrieve the size information of a selected region after making the selection. Additionally, an auto update option is available to automatically generate the selected size after each paint brush operation.
  • A table control is added to the paint brush dialog to display the size information of the selected region. A list of selection history can be kept when the history option is turned on.
  • A table control is added to the component analysis dialog to display the results from component analysis. Each information entry is aligned with the table header; the table cell of the component ID is colored based on the component color.
  • An option to enable the accuracy mode for paint selection when there are multiple bricks. When the brick selection accuracy mode is turned on, diffusion can go cross brick borders but is time consuming. Turn off this option for faster selection operations.
  • High transparency mode for volume properties. High transparency mode is an alternative to the MIP mode. It increases the transparency for low intensity signals.
  • New color maps. We added three new color maps specifically designed for rendering structures against light colored background: Low-key, High-key, and High transparency. These color maps are recommended to be used together with the high transparency mode.
  • Color map inversion. We added an option to invert any color maps. Previously inverted color maps (for rainbow etc.) were only available as predefined color maps.
  • Background color inversion. We added an option to invert the background color.
  • Color map legend option. We added an option to the render view that allows the color map legend to be turned on and off.
  • Color map in the depth mode. Color maps can be applied to multiple channels in the depth mode. Different channels can have individually controlled color maps in the depth mode.
  • Component color shuffling. In the component analysis dialog and the tracking dialog, we added a button to shuffle the colors after component generation. It allows better distinction of different components.
  • Improvements to component generation on selected regions. When a region is selected by brush and component analysis is applied to the region, components outside of the region are unaffected. Previously, the component IDs outside of the selected region were set to zeros after component analysis.
  • Simplification of the volume count and noise reduction dialogs. Most of the functions have also become available in the brush and component analysis dialogs.
  • New 4D script for semi automatic tracking. Choose the semi auto tracking script from the movie/export panel and semi automatic tracking has been made easier to use. Select structures, single or multiple, from one time point and advance in time. The selected structures are automatically segmented and linked with the new script. The auto link and assign functions from previous versions, which only allows to track single structure manually, have been removed.
  • Redesign of the 4D script structure. We have redesigned the structure of the 4D scripts to accommodate more complex behaviors.
  • Flip ruler point order. We added an option in the measurement dialog to flip the order of the points on a ruler. Use this feature to reorganize the ruler point orders to better suit further analysis in Excel when rulers are exported.
  • Shading improvement. We have improved the parameters for shading in volume properties. The transition between shaded and unshaded volume channel is smooth.
  • Expanded shadow effect. We have expanded the shadow region for the effect. It gives a more pronounced shadow effect but may slow down rendering on less powerful computers.
  • Adjustments to the user interface. We have moved the clear selection button for the paint brush selection, so that it is less likely to be clicked by mistake. We have resolved the flickering issue of some user interface controls. The high shading parameter is grouped together with the shading blending factor.

We also fixed the following issues:

  • A structure moving a large distance between two time points was not tracked because of no overlapping. We have expanded the search region for unlinked structures.
  • Component size limit could not be set over 100 in the tracking dialog. We have expanded the range of the size setting.
  • Volume data in the Nrrd format could not be loaded correctly when the data type is unsigned short. We have fixed the issue to support Nrrd data of unsigned short type.
  • The text of the scale bar may not be displayed correctly when the text is turned on before loading data.
  • Extracted volume data became over saturated when the data type is 16-bit. We have fixed the issue so that extracted data are following the bit depth of the original data and scaled properly.
  • Program hangs when both mesh data and volume data are being deleted. We have fixed the issue so that both mesh data and volume data can be deleted.

FluoRender v2.23.3 Released

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Thank you for using FluoRender. Download the installer package for your operating system (Windows or macOS) from the list of assets.

FluoRender v2.23.3 has made several usability improvements over the previous v2.23 minor releases. The new features include:

  • Brush operation keep 16-bit data
    When you use the brush tool on a volume channel and extract or erase part of the volume, the derived volume channel will have the same bit depth as the original channel.
  • Export coordinates for each ruler point
    When you export rulers with more than two points, it saves the coordinates of each ruler point along with other ruler information.
  • Improved density-based component generation
    A density field is generated and locally equalized for separating distinct structures in component generation/segmentation. The segmentation accuracy has been improved for data sets with uneven brightness.
  • Improved EM clustering method
    The EM clustering can be initialized with the result from the K-means clustering or manual segmentation. It is useful for segmenting more than two ellipsoid shaped objects. Additionally, signal intensity variation has been added to the calculation for the EM method.
  • Added a distance field option for component generation
    A distance field is generated and can be intermixed with the original intensity and/or the density field. The segmentation accuracy has been improved for data sets with strongly connected structures that are intended to be separated.
  • Compute distance between a locator and segmented components
    You can create a locator and compute its distances to all analyzed components. Analyze components before applying this function.
  • Compute a distance adjacency matrix among components
    You can compute a distance adjacency matrix representing all pairwise distances of analyzed components. The adjacency matrix can be also filtered to only include nearest neighbors. Analyze components before applying this function.
  • A new ellipse ruler tool
    You can add an ellipse ruler and retrieve its center coordinates. It is useful for measuring an empty space, such as a hole, in a data set.
  • Component generation functions have been reorganized
    The old basic and slice-based functions have been consolidated into a single page of settings. The new setting page includes settings for intensity threshold, density field, distance field, and clean up. Additionally, intermediate results can be fixated to prevent further merging after parameter changes. A macro recorder is added to automate and streamline multistep segmentation operations. A recorded command can be applied to similar data sets or a time sequence.
  • Copy and paste locator center coordinates
    The center coordinates of a ruler tool can be copied using the common shortcuts, such as Ctrl+C or Cmd+C, and pasted into Excel. Center coordinates of locator can be edited by typing or pasting the XYZ coordinate values. The clipboard format for the XYZ coordinates is compatible with Excel.
  • An auto update setting for component generation
    An auto update setting can be enabled for component generation. Once enabled, changes to the component generation settings are immediately applied and displayed. A fast GPU is expected for this feature to work smoothly.
  • An average tool for center of ruler tools
    You can create a locator tool and have its location set at the center of a series of rulers.
  • Multichannel colocalization
    You can compute the colocalization of many channels at once. An adjacency matrix representing the colocalization is computed and saved an Excel-compatible file.

FluoRender v2.23.3 addresses these issues:

  • FluoRender crashes when a project is loaded and there are existing data.
  • FluoRender does not update to the next/previous time point when the brush tool is enabled from the toolbar.
  • Automatic OpenCL platform selection may not infer the correct platform. A manual setting in the setting file is therefore enabled.
  • The scale bar is not positioned and scaled correctly when a screen capture is enlarged.
  • Data outside of the clipping planes are not excluded from component analysis.
  • Extremely high system memory consumption for tracking densely packed data.

Previously, FluoRender v2.23.1 added these new features:

  • Fiji support
    An expanded file format support is available by configuring FluoRender to use Fiji’s functions. Since Fiji includes Bioformats in its package, settings to link with Fiji have been simplified.

And FluoRender v2.23.0 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
    You can configure a zoom ratio for the rotation center anchoring to become active. You 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 ΔF/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 FluoRender v2.23.0 addressed 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.