napari 0.4.1

We’re happy to announce the release of napari 0.4.1! napari is a fast, interactive, multi-dimensional image viewer for Python. It’s designed for browsing, annotating, and analyzing large multi-dimensional images. It’s built on top of Qt (for the GUI), vispy (for performant GPU-based rendering), and the scientific Python stack (numpy, scipy).

For more information, examples, and documentation, please visit our website: https://github.com/napari/napari

Highlights

This release follows our recent 0.4.0 release with a number of bug fixes and small improvements. We fixed a regression that caused the status bar to always display information from the topmost layer, rather than the selected layer. We’ve also added new minimum and average intensity projection rendering modes for volumetric data. Finally, we made some useful visual improvements, such as displaying text labels identifying axes on our axes visual, and colorbars in our colormap selection dropdown to make colormap selection easier.

A small note: we have temporarily disabled the viewer’s welcome visual while we investigate some crashes that it seemed to be contributing to. See #1905.

New Features

  • Live tiff loader example (#1610)

  • Add NAPARI_EXIT_ON_ERROR (#1812)

  • Add text labels to axes (#1860)

  • Add minimum intensity projection shader to 3d rendering mode (#1861)

  • Average intensity projection shader for 3d rendering (#1871)

Improvements

  • Integrated plugin dialog with install/uninstall & remote discovery (#1357)

  • Use TypedEventedList and TypedList for LayerList and TransformChain (#1504)

  • Add checkbox to labels layer controls for displaying selected color mode (#1762)

  • Async-17: MiniMap (#1774)

  • Async-18: Basic Quadtree Rendering (#1793)

  • Mouse callback examples tweaks (#1796)

  • Simplify viewer and make headless mode easier (#1808)

  • Move viewer keybindings (#1810)

  • Async-19: Minimap and Test Images (#1813)

  • Pre-sort tracks data by ID and time (#1814)

  • Enhance affine example to include scipy.ndimage (#1815)

  • Sort tracks and track properties by ID then t (#1818)

  • Add a simple grid object (#1821)

  • Add example: visualize 2d+timelapse as 3D space-time images, a.k.a. “kymographs” (#1831)

  • Async-20: Better QtTestImage (#1834)

  • Async-21: TiledImageVisual with Texture Atlas (#1837)

  • Return estimate for 3D texture size instead of hard-coded value (#1857)

  • Drop old typed list (#1859)

  • Colormap presentation in dropdown list (#1862)

  • Async-22: Support Edge/Corner Tiles (#1867)

  • Async-23: QtRender Fixes (#1870)

  • Async-24: Multiscale Octree w/ Async Loading (Golden Spike) (#1876)

  • Add reverse gray colormap (#1879)

  • Async-25: Remove VispyCompoundImageLayer (#1890)

  • Async-26: Artificial Delay and fixes (#1891)

  • Add properties event (#1896)

  • Async-27: Sparse Octree (#1892)

  • Standardize grid events (#1926)

Bug Fixes

  • Fix zoom of scale bar and axes visuals on launch (#1791)

  • Fix ValueError in Layer.coordinates during layer load (#1798)

  • Fix TransformChain.init() (#1809)

  • Fix #1811: Move visual creation to end of init (#1835)

  • Fix keybinding inheritance (#1838)

  • Fix lower triangular shear values (#1839)

  • Fix bug for painting when scale above 1 (#1840)

  • Enhance accessibility by ensuring welcome screen contrast meets required standards (#1863)

  • Apply requested opacity in points layer (#1864)

  • Fix active layer update (#1882)

  • Fix affine composition order (#1884)

  • Fix affine warning (#1886)

  • Fix Py3.9 Big Sur bug (#1894)

  • Make control of grouping part of public api again (#1895)

  • Fix windows plugin dupe (#1899)

  • Revert #1857 “Return estimate for 3D texture size instead of hard-coded value” (#1907)

  • Hide welcome visual (#1922)

API Changes

  • Viewer.grid_view() and Viewer.stack_view() are deprecated. Instead, use viewer.grid.enabled = <True/False>. (#1821)

  • Viewer.grid_stride and Viewer.grid_size are deprecated. Instead, use Viewer.grid.stride and Viewer.grid.shape. (#1821, #1847)

Build Tools and Docs

  • Update setup.cfg to add aliases for pyqt5 and pyside in extras_require (#1795)

  • Unpin qt, exclude 5.15.0 (#1804)

  • Allow ability to run all tests on local Windows installs (#1807)

  • Try different test for popup skipif mark (#1817)

  • Fix image.sc badge link to forum (#1828)

  • Fix bundle build by adding sudo for disk detach (#1844)

  • Patch mac bundle differently (#1848)

  • Bump qtconsole version requirement to fix #1854 (#1855)

  • Update set-env in make_release action (#1897)

  • Fix set-env for bundle build (#1901)

  • Fix linux bundle by linking gdbm library 3 to 5 (#1918)

  • Pin Pyside2 5.15.1 for linux CI and bundle build (#1925)

  • Update documentation for the nightly build release (#1932)

  • Install specific PySide version when building bundle (#1936)

  • Unpin Pyside2 5.15.1 and revert #1925 (#1937)

  • Add pims to bundle (#1939)

18 authors added to this release (alphabetical)

10 reviewers added to this release (alphabetical)

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