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Recent Releases of lls-core

lls-core - v1.0.3

What's Changed

  • Add docs for napari plugin by @pr4deepr in https://github.com/BioimageAnalysisCoreWEHI/napari_lattice/pull/101
  • Adding an option to apply quick deskew. Only works in 3D view by @pr4deepr in https://github.com/BioimageAnalysisCoreWEHI/napari_lattice/pull/102
  • Updated docs to include more information by @pr4deepr in https://github.com/BioimageAnalysisCoreWEHI/napari_lattice/pull/107

Full Changelog: https://github.com/BioimageAnalysisCoreWEHI/napari_lattice/compare/v1.0.2...v1.0.3

- Jupyter Notebook
Published by pr4deepr 12 months ago

lls-core - v1.0.2

Added release version for pypi

Full Changelog: https://github.com/BioimageAnalysisCoreWEHI/napari_lattice/compare/v1.0.1...v1.0.2

- Jupyter Notebook
Published by pr4deepr about 1 year ago

lls-core - v1.0.1

What's Changed

  • Fixdependency by @pr4deepr in https://github.com/BioimageAnalysisCoreWEHI/naparilattice/pull/98
  • Updated docs by @multimeric in https://github.com/BioimageAnalysisCoreWEHI/napari_lattice/pull/93

Removed Python 3.11 support for napari plugin temporarily due to dependency conflicts related to napari-aicsimageio. The CLI lls-core should work fine on Python 3.11.

Full Changelog: https://github.com/BioimageAnalysisCoreWEHI/napari_lattice/compare/v1.0.0...v1.0.1

- Jupyter Notebook
Published by pr4deepr about 1 year ago

lls-core - v1.0.0

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

lls-core - Minor bugfix

Fixed bug when reading PSFs: https://forum.image.sc/t/llszwidget-error-in-napari-lattice/79823

- Jupyter Notebook
Published by pr4deepr almost 3 years ago

lls-core - Major fixes: Better interpolation!

MAJOR UPDATES:

  • BUG FIX: Orthogonal interpolation is enabled by default. Thanks to @haesleinhuepf for helping implement this in pyclesperanto-prototype https://github.com/clEsperanto/pyclesperanto_prototype/issues/196. Thanks to @dpshepherd for his help as well. This will get rid of edge artefacts with highly anisotropic data.
  • Changed GUI so GPU option and deskew angle are now within the Initialize button Dialog Box.
  • Can now choose GPU option when Initializing napari plugin
  • @DrLachie added support for running napari-lattice from the HPC, and fixed bugs in the batch processing section
  • Updated notebooks

Tests: * Fixed Github workflows so it should work with QT tests * Added more tests for deskewing, cropping and testing batch processing using napari-lattice

### References for orthogonal interpolation: * Sapoznik et al., 2020 * qi2lab-OPM

- Jupyter Notebook
Published by pr4deepr about 3 years ago

lls-core - minor bugfix

  • @DrLachie fixed a bug with workflows when using napari_lattice in the terminal
  • Added dependabot so it keeps dependencies up to date in github actions

- Jupyter Notebook
Published by pr4deepr about 3 years ago

lls-core - v0.2.4

  • Fixed bugs with reading channels and time ranges
  • Added support for using config files when running from terminal https://github.com/BioimageAnalysisCoreWEHI/napari_lattice/issues/12
  • Added functionality to process single ImageJ roi files (.roi) files in addition to ImageJ roi zip files.

Minor: - Logging instead of print statements

Had to update release from 0.2.2a to 0.2.4 as we wanted 0.2.4 to be the default install

Contributors: @pr4deepr and @DrLachie

- Jupyter Notebook
Published by pr4deepr over 3 years ago

lls-core - v0.2.1-a

  • Fixed edge artefacts when performing deconvolution using pycudadecon https://github.com/BioimageAnalysisCoreWEHI/napari_lattice/commit/e87095dd661aa4879951eb048964dea4f4a5a8cd
  • Fixed h5 saving so any channel range and time range can be saved https://github.com/BioimageAnalysisCoreWEHI/napari_lattice/commit/744e1b64841c03ebc6fab219a588d9ab32bc00fb
  • Added example notebooks for deconvolution https://github.com/BioimageAnalysisCoreWEHI/napari_lattice/commit/eff3901b669e7468a7cf80d9de0be7826cec3a9e
  • Cropping is no agnostic to skew direction. Should work on skew direction of X or Y.
  • Fixed Not a tiff file error when reading psfs for czi https://github.com/BioimageAnalysisCoreWEHI/napari_lattice/commit/6d54ef7e68b0fe7a31073b4f23c563fb4e80b5a4
  • Widget for Preview Deskew is now collapsible
  • Only the main Cropping Widget is scrollable.

- Jupyter Notebook
Published by pr4deepr over 3 years ago

lls-core - v0.2.0

  • Added napari spreadsheets as dependency to enable easy preview of tables when using "Preview Workflows" on workflows that return tables.
  • Added wiki and examples for generating workflows using napari-assistant
  • Added wiki and examples for using CellPose for segmenting lattice lightsheet data

- Jupyter Notebook
Published by pr4deepr over 3 years ago

lls-core - napari_lattice v0.1.8

  • Fixed bugs with deconvolution using pycudadecon
  • Added deconvolution when using workflows. This should also be active when running napari-lattice in the terminal
  • updated fsspec to fix czireader error

- Jupyter Notebook
Published by pr4deepr over 3 years ago

lls-core - first_release

This is the first release for napari lattice plugin. It is still in experimental phase and will have breaking changes in future release.

- Jupyter Notebook
Published by pr4deepr over 3 years ago