v4.17.1

Changes

• Updated DCMTK to version 3.7.0 on Linux fixing bug with error when opening files.
• Added support for batch-wise processing in SegmentationNetwork.
• Added maxBatchSize argument to neural network create methods.
• Added ProcessObject::getOutput to pyfast.

Download and Install

Release binaries and installers can be downloaded below by pressing "assets". Make sure you have the required dependencies installed on your system before using the release: see the installation instructions for Windows, Ubuntu Linux, macOS and Docker containers.

v4.17.0

Changes

• Fixed crucial bug introduced in v4.16.1 where color images downsampled with ImageResizer became grayscale. This is now fixed by adding multi-channel support to GaussianSmoothing.
• Added per image channel support in ZeroMeanUnitVariance. On by default.
• Added output instance segmentation option to RegionProperties and fixed typo in Region variable perimeterLength.
• Added new RemoveRegions PO, and modified LabelModifier with new constructor and uint > 8bit support.
• Moved RegionProperties to new Region folder.
• Added title, fullscreen and maximize arguments to display shortcuts functions.
• Added Otsu thresholding method.
• Moved BinaryThresholding to new Thresholding folder.
• Added normalize first option and 3D support to ImageCaster.
• Modified ProcessObject::run() to return pointer to process object, and added the ProcessObject::getOutput method. ProcessObject::update marked as deprecated.

Download and Install

Release binaries and installers can be downloaded below by pressing "assets". Make sure you have the required dependencies installed on your system before using the release: see the installation instructions for Windows, Ubuntu Linux, macOS and Docker containers.

v4.16.1

Changes

• Improved speed of PatchGenerator when a mask (input port 1) was provided.
• Added anisotropic support to GaussianSmoothing.
• Added blur on downsampling feature to ImageResizer option (on by default).

Known issues

• This version introduced a bug in ImageResizer where color images becomes grayscale if downsampling. Version 4.17.0 fixes this bug.

Download and Install

Release binaries and installers can be downloaded below by pressing "assets". Make sure you have the required dependencies installed on your system before using the release: see the installation instructions for Windows, Ubuntu Linux, macOS and Docker containers.

v4.16.0

Changes

• A new high-level interface to OpenCL has been added, which makes it even easier to do OpenCL processing in process objects in both C++ and Python. A tutorial on this interface was added the documentation page.
• Implemented ImagePyramid::getLevelSizes(), added some more ImagePyramid tests, and added additional checks to constructor when levelSizes is provided.
• Refactored OpenCL binary caching mechanism.
• Added support for using vertex label in VertexRenderer assigning color per label.
• Improved Mesh; making normals, colors and normals optional.
• Added integer and unsigned integer conversion support to Eigen Python typemaps.
• Added min and max options to ImageInverter and fixed a bug with minimum intensity.
• Added getAbsolutePath utility function.
• Added missing spacing in translation of image in getPatchAsImage.

Download and Install

Release binaries and installers can be downloaded below by pressing "assets". Make sure you have the required dependencies installed on your system before using the release: see the installation instructions for Windows, Ubuntu Linux, macOS and Docker containers.

v4.15.1

This is only a minor patch update.

Changes

• Copy/Move image data to host, not default device, when getting a raw or unique pointer to data. This removes some unnecessary CPU->GPU->CPU memory transfers.
• Disable compression not supported warning with TIFF.
• Added detailed runtime measurements in ImagePyramidAccess object.

Download and Install

Release binaries and installers can be downloaded below by pressing "assets". Make sure you have the required dependencies installed on your system before using the release: see the installation instructions for Windows, Ubuntu Linux, macOS and Docker containers.

v4.15.0

Changes

• Added the display2D and display3D shortcut functions to both Python and C++ version of FAST for reducing boiler plate code when displaying data (see example below).
• Added support for PyTorch tensors in Image and Tensor in pyFAST with the two functions fast.Image.createFromTensor and fast.Tensor.createFromTensor.
• Fixed bug in DicomMultiFrameStreamer.
• Renamed DicomMultiFrameStreamer to DICOMMultiFrameStreamer, and FAST_MODULE_Dicom to FAST_MODULE_DICOM.
• Upgraded DCMTK on macOS arm64 to 3.6.9.
• Added possibility of specifying another image pyramid structure in ImagePyramid::create than the default downsample by factor 2.
• Removed check that removes any image pyramid levels less than 4 MB when importing with OpenSlide.
• macOS x86_64 builds are now done on macOS 15 since macOS 13 runner on github is being removed.

New display2D and display3D shortcut functions

Instead of this:

renderer1 = fast.ImageRenderer.create().connect(image)
renderer2 = fast.SegmentationRenderer.create(opacity=0.25).connect(segmentation)
fast.SimpleWindow2D.create(bgcolor=fast.Color.Black()).connect([renderer1, renderer2]).run()

You can now just do this:

fast.display2D(image, segmentation, segmentationOpacity=0.25, bgcolor=fast.Color.Black())

A 3D version display3D also exists. And these functions are also available for C++.

Download and Install

Release binaries and installers can be downloaded below by pressing "assets". Make sure you have the required dependencies installed on your system before using the release: see the installation instructions for Windows, Ubuntu Linux, macOS and Docker containers.

v4.14.1

Changes

• Added --no-gui command line option to systemCheck tool.
• Throw exception when importing with OpenSlide and nr of levels is < 1, which can happen when importing dicom WSIs.
• Made estimation of magnification from spacing optional in ImagePyramid::getMagnification, default is false.
• Throw exception in DrawCircle if no centroids or radius were given.

Download and Install

Release binaries and installers can be downloaded below by pressing "assets". Make sure you have the required dependencies installed on your system before using the release: see the installation instructions for Windows, Ubuntu Linux and macOS.

v4.14.0

Changes

• Use zlib-ng instead of standard zlib which improves zraw and nii.gz decompression and compression runtime.
• Use libjpeg-turbo on windows which give improved jpeg decompression and compression runtime performance.
• Use bundled tiff and libjpeg-turbo on mac which removes the need for using brew.
• Added 2D support to ImageInverter.
• Added pixel connectivity option to SeededRegionGrowing.
• Implemented FillHoles, DrawCircle and DrawCubicHermiteSpline process objects.
• Fixed bug in getModifiedDate used when checking if OpenCL kernels need to be recompiled on windows.

Download and Install

Release binaries and installers can be downloaded below by pressing "assets". Make sure you have the required dependencies installed on your system before using the release: see the installation instructions for Windows, Ubuntu Linux and macOS.

v4.13.1

Changes

• Fixed potential seg fault when importing OME-TIFF files.
• Large performance improvements of ImagePyramidAccess and PatchGenerator when reading TIFF files. This was achieved by fixing some bugs, nested loop optimizations and tile caching.
• Moved runtime measurement from ProcessObject to Object.
• Some code cleanup

Download and Install

Release binaries and installers can be downloaded below by pressing "assets". Make sure you have the required dependencies installed on your system before using the release: see the installation instructions for Windows, Ubuntu Linux and macOS.

v4.13.0

Changes

• Implemented support for reading JPEG compressed TIFF files where the JPEG tables are stored globally in the JPEGTables tag instead of for each tile.
• Added TextWidget; a simple object for adding text and variables to a window.
• Added possibility of giving vertex point size in millimeters to the VertexRenderer.
• Added opacity parameter to VertexRenderer.
• Added extractContours parameter to RegionProperties.
• DataHub download and getItem no longer requires internet connection, if files are already downloaded.
• Fixed bug with image pyramid and segmentation rendering not working with RenderToImage.
• Fixed bug in PatchGenerator and TissueSegmentation when generating only one image patch.
• Fixed bug in Mesh when updating data on host.
• Fixed bug with stopPipeline in PythonProcessObject in pyfast.
• Fixed bug with CL-GL interoperability on windows.

Download and Install

Release binaries and installers can be downloaded below by pressing "assets". Make sure you have the required dependencies installed on your system before using the release: see the installation instructions for Windows, Ubuntu Linux and macOS