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@basisunus basisunus released this May 11, 2020

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.
Assets 6

@basisunus basisunus released this Apr 3, 2020 · 184 commits to master since this release

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.
Assets 6

@basisunus basisunus released this Jan 10, 2020 · 184 commits to master since this release

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.
Assets 6

@basisunus basisunus released this Oct 23, 2019 · 268 commits to master since this release

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.
Assets 6

@basisunus basisunus released this Aug 30, 2019 · 320 commits to master since this release

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.
Assets 6

@basisunus basisunus released this Jun 11, 2019 · 455 commits to master since this release

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.
Assets 6

@basisunus basisunus released this Dec 10, 2018 · 560 commits to master since this release

Download the installation packages under "Assets". Choose FluoRender2.23.1_win64.exe for Microsoft Windows 7, 8, 8.1, and 10. Choose FluoRender2.23.1_mac64.pkg for Apple OS X or macOS 10.9 and above.

FluoRender Version 2.23.1 added these new features:
• Fiji support. Enable ImageJ or Fiji in the settings. Then, load files with the "ImageJ Import" button.

This version also fixed other minor issues.

Assets 6

@basisunus basisunus released this Aug 13, 2018 · 623 commits to master since this release

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.

Assets 6

@basisunus basisunus released this Mar 27, 2018 · 793 commits to master since this release

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.

Assets 6

@basisunus basisunus released this Nov 1, 2017 · 895 commits to master since this release

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.

Assets 6
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