8. What’s new?

8.1. Version 1.2.1

8.1.1. Highlights

  • New Image loading/saving interface to load/save full 5D images (no display yet though)
  • Direct interfacing to Image Magick to load images, allowing finer control and faster image loading.

8.1.2. Details

  • Corrected the auto-update dialog box (Pull Request 21)
  • Corrected installation message of Image Magick (Pull Request 21)
  • Corrected handling of spaces in path to Python (windows only) (Pull Request 22)
  • Restored cutting surfaces, as v. 1.2.0 has a typo in the shaders. (Pull Request 23)
  • Completly new Image5D object for loading/saving images. This means processes can now load and process full 5D images (Pull Request 24)
  • Auto-seeded mesh segmentation now clear the old segmentation (Pull Request 25)
  • Corrected handling of the Delete and Backspace keys in the main GUI (Pull Request 25)
  • Python macros can now be documented using the module’s documentation (Pull Request 25)
  • New python module plyfile in lgxUtils package to load PLY files (e.g. meshes) (Pull Request 25)
  • Information::out and Information::err are now thread-safe (Pull Request 26)
  • Correction of 3D picking (it was shifted by half a voxel) (Pull Request 27)
  • Corrected use of Image Magick to prevent gamma correction when loading (Pull Request 27)
  • lgx::util::apply_kernel_it can now accept a kernel by rvalue reference too.
  • When installing directly a source package, a copy of the source is kept for future re-compilation, but is currently not used (Pull Request 28)
  • If a plugin fails to load, LithoGraphX will try again to load it at the next launch (Pull Request 28).
  • Started the documentation of the plugins and packaging system (Pull Request 29).
  • Added samples plugins to installation (Pull Request 29)
  • Added notes to not use named arguments in sip as it wasn’t available for Qt 5.2 (Pull Request 30)
  • Improved checking of package dependencies, added option to force (un-)installation (Pull request 31).
  • Optimized image sequence loading using Image Magick’s capability to load many files at once (Pull Request 32).

8.2. Version 1.2.0

8.2.1. Highlights

  • New Packaging system to distribute processes
  • New Plugin system with interface to manager them
  • Improved cell classification processes
  • Optimization if ITK algorithms for 2D images
  • New incremental auto-seeded watershed

8.2.2. Details

  • Corrected reading RGB TIFFs and OME-TIFFs generated by the Zeiss software (Pull Request 1).
  • Watershed can now be used on partially segmented stacks (Pull Request 2).
  • Transfer function is now copied with the meta data of a store (Pull Request 3).
  • Swap / Copy stacks handles small differences (e.g. less than noise) in step and origin correctly (Pull Request 3).
  • Corrected cutting surfaces (Pull request 4).
  • Improved Segment Section process: when inverting the image, it is reverted before exiting the process (Pull Request 5).
  • Documented Shader class, also minor improvements of this class (Pull Request 5).
  • Correction PC analysis: PCs are now ordered properly (Pull request 6)
  • Split Ubuntu packages into dev, doc and bin and added versioning of shared object files (Pull Request 7).
  • Now all ITK algorithms are instanciated explicitely for 2D images if one of the dimension is 1, it’s faster and works more often (some 3D algorithms require a real 3D image) (Pull Request 8).
  • Corrected the use of copyMetaData in ITK algorithms (Pull Request 8).
  • Correctly compiles with newer version of ITK and CUDA (Pull Request 9).
  • Improvements in cell classifier UI: the GUI has been fully revised and what was “suffixes” can now be Python’s formatting expressions (Pull Request 10).
  • Cell classifiers can now use project files to read the transformation before generating the features (Pull Request 10).
  • The CSV reader now also understands if the CSV uses semi-colons instead of comas (looking at you Microsoft Excel) and it works if there is only one columns (Pull Request 11).
  • The windows version now finds the correct version of Python (Pull Request 12).
  • ITK segmentation now sets the labels flag properly (Pull Request 13).
  • New section about hardware specification in the documentation (Pull Request 14).
  • Corrected computation of the incline angle for 2d cell features to be in the range from -pi/2 to pi/2 (Pull Request 15).
  • The cell classifier has been moved to Global processes to allow use of cells from stacks or meshes and change the transformation (Pull Request 16).
  • Added packaging system and plugin management (Pull Request 18 and Pull Request 19).
  • For windows, added a building environment (Pull Request 18).
  • Added new tutorial on “flat” cells segmentation (Pull Request 18).
  • Corrected problem with drawing when selecting cells (Pull Request 18).
  • Corrected rendering of Pixel Edit’s circle (Pull Request 19).
  • Added dialog box to use laptop or desktop configuration the first time LithoGraphX is launched (Pull Request 19).
  • Updated tutorials with new presentation of used processes (Pull Request 19).
  • Thrust can now compile in CPU mode, in which case CLang can be used (Pull Request 19).
  • Under windows, the installer register LithoGraphX to the local installation of cmake (Pull Request 19).
  • All tools now have keyboard shortcuts (Pull Request 19).
  • Under windows, the installer now offers to also install Image Magick (Pull Request 19).
  • Add new “What’s new?” section in the documentation (Pull Request 20).
  • When a new version of LithoGraphX appears, the About box appears before the interface (Pull Request 20).