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Release History

PyPI version Downloads

Below, you'll find details about the version history of qim3d.

Remember to keep your pip installation up to date so that you have the latest features!

v1.2.0 (31/03/2025)

  • Switched from setup.py to pyproject.toml

  • Updated mesh generation from volumes

v1.1.2 (07/03/2025)

  • Update and refactoring for 3D U-Net architectures

  • Background noise generation for synthetic images

v1.1.1 (27/02/2025)

  • Refactored the synthetic data generation module

v1.1.0 (26/02/2025)

  • Source repo moved to GitHub

  • Line profile tool

line profile

  • Threshold exploration tool

threshold exploration

v1.0.1 (10/02/2025)

  • Fixed missing requirements

v1.0.0 (21/01/2025)

  • First stable release of the library, with significant refactoring.
  • Layout and organizational update for the documentation.
  • Additional coverage for unit tests.

v0.4.5 (21/11/2024)

  • Updated Layer surface segmentation GUI
  • Sphericity as feature from volumes
  • Colorbar for visualization functions
  • Chunk visualization tool
  • Histogram visualization

v0.4.4 (11/10/2024)

  • Introduction of itk-vtk-viewer for OME-Zarr data visualization 🎉 itk-vtk-viewer

v0.4.3 (02/10/2024)

  • Updated requirements
  • Introduction of mesh generation, visualization, saving and loading 🎉 Mesh generation

v0.4.2 (30/09/2024)

  • Export and import is now possible in the OME-Zarr standard, including multi-scale datasets.
  • Filters now have the option to use Dask when available Filters with dask

v0.4.1 (30/07/2024)

  • Fixed issue with example volumes not being loaded

v0.4.0 (29/07/2024)

  • Refactored imports to use lazy loading
  • Namespace utils reserved for internal tools only
  • All deep-learning related functions moved to models
  • Running pip install qim3d does not install DL requirements. For those, use pip install qim3d['deep-learning']

v0.3.9 (24/07/2024)

  • Loading and saving for Zarr files
  • File convertion using the CLI, including Zarr
  • Refactoring for the GUIs
  • Color visualization for structure tensor Color visualization for structure tensor
  • Refactoring for synthetic data generation, from utils to generate
  • Introduction of qim3d.generate.collection 🎉 Introduction of qim3d.generate.collection

v0.3.8 (20/06/2024)

  • Minor refactoring and bug fixes

v0.3.7 (17/06/2024)

  • Performance improvements when importing
  • Refactoring for blob detection Refactoring for blob detection

v0.3.6 (30/05/2024)

  • Refactoring for performance improvement
  • Welcome message for the CLI
  • Introduction of qim3d.processing.fade_mask 🎉 Introduction of qim3d.processing.fade_mask

v0.3.5 (27/05/2024)

  • Added runtime and memory usage in the documentation
  • Introduction of qim3d.utils.generate_volume 🎉 Introduction of qim3d.utils.generate_volume
  • CLI refactoring, adding welcome message to the user CLI refactoring
  • Introduction of preview CLI 🎉

v0.3.4 (22/05/2024)

  • Documentation for qim3d.viz.plot_cc
  • Fixed issue with Annotation tool and recent Gradio versions
  • New colormap: qim3d.viz.colormaps.qim, showcasing the Qim colors!
  • Object separation using qim3d.processing.operations.watershed
  • Added option to pass dim_order to vol/vgi files
  • The 'Data Explorer' GUI now can load image sequences also
  • Warning in case user tries to load a file larger than available memory
  • Objects colormap now can enforce a min_dist between neighbor colors
  • It is possible to load a directory with a sequence of PIL images
  • Aspect ratio issue for k3d fixed

v0.3.3 (11/04/2024)

  • Introduction of qim3d.viz.slicer (and also qim3d.viz.orthogonal ) 🎉
  • Introduction of qim3d.gui.annotation_tool 🎉
  • Introduction of qim3d.processing.Blob for blob detection 🎉
  • Introduction of qim3d.processing.local_thickness 🎉
  • Introduction of qim3d.processing.structure_tensor 🎉
  • Support for loading DICOM files with qim3d.io.load
  • Introduction of qim3d.processing.get_3d_cc for 3D connected components and qim3d.viz.plot_cc for associated visualization 🎉
  • Introduction of qim3d.viz.colormaps for easy visualization of e.g. multi-label segmentation results 🎉
  • Introduction of qim3d.processing.operations.background_removal 🎉
  • Documentation refactoring
  • Fixed bug preventing Data Explorer to show files

v0.3.2 (23/02/2024)

This version focus on the increased usability of the qim3d library

  • Online documentation available at https://platform.qim.dk/qim3d
  • Virtual stacks also available for txm files
  • Updated GUI launch pipeline
  • New functionalities for qim3d.viz.slices_grid
  • Introduction of qim3d.processing.filters 🎉
  • Introduction of qim3d.viz.vol 🎉

v0.3.1 (01/02/2024)

Release expanding the IO functionalities

  • Support for loading vol nii and bigtiff files
  • Data loader now supports virtual_stack
  • Save functionality for all file formats except txm

v0.3.0 (23/01/2024)

  • Introduction of qim3d CLI 🎉
  • Introduction of memory utils 🎉
  • Data Explorer GUI
  • Save functionality for tif files

v0.2.0 (18/09/2023)

Includes new develoments toward the usability of the library, as well as its integration with the QIM platform.

  • Refactored code for the graphical interfaces
    • For the local thicknes GUI, now it is possible to pass and receive numpy arrays instead of using the upload functionality.
  • Improved data loader
    • Now the extensions tif, h5 and txm are supported.
  • Added qim3d.viz.slices_grid for easy slice visualization.
  • U-net model creation
    • Model availabe from qim3d.models.UNet
    • Data augmentation class at qim3d.utils.Augmentation
    • Notebook with full pipeline at docs/notebooks/Unet.ipynb
  • Image examples accessible from qim3d.examples

v0.1.3 (17/05/2023)

First stable release.

  • Simple Tiff data loader
  • Graphical interfaces
    • Local thickness
    • 3D Isosurfaces
    • Data exploration tool