https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.22.1

Bugfix: * Setting voxel size of 2D images raised an error.

- Python
Published by haesleinhuepf over 3 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.22.0

Changed menu locations * Some menus have been moved from Measurement to Measurement tables and Measurement maps

- Python
Published by haesleinhuepf over 3 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.21.2

New menu entries * Segmentation post-processing > Merge annotated touching labels

- Python
Published by haesleinhuepf over 3 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.21.1

New menu entries (Thanks to Varun Kapoor for proposing) * Transform > Rotate * Transform > Reduce stack * Transform > Sub-stack * Transform > Scale * Transform > Translate * Transform > Rigid Transform

- Python
Published by haesleinhuepf over 3 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.21.0

New features, added to the menu: * Tools > Filtering / background removal > Top-hat (box, clesperanto) * Tools > Filtering > Difference of Gaussian (clesperanto) * Tools > Filtering > Laplacian of Gaussian (clesperanto) * Tools > Filtering / background removal > Subtract Gaussian background (clesperanto) * Tools > Filtering / background removal > Divide by Gaussian background (clesperanto) * Tools > Filtering > Small Hessian eigenvalue (clesperanto) * Tools > Filtering > Large Hessian eigenvalue (clesperanto) * Tools > Filtering / edge enhancement > Standard deviation (box, clesperanto) * Tools > Filtering / edge enhancement > Variance (box, clesperanto) * Tools > Measurement > Extension ratio map (clesperanto) * Tools > Measurement > Pixel count map (clesperanto) * Tools > Image math> Reciprocal (clesperanto) * Tools > Image math > Absolute difference (clesperanto) * Tools > Image math > Squared difference (clesperanto) * Tools > Segmentation / labeling > Eroded-Otsu-labeling (clesperanto) * Tools > Segmentation / labeling > Gauss-Otsu-labeling (clesperanto) * Tools > Segmentation post-processing > Binary AND / intersection (clesperanto) * Tools > Segmentation post-processing > Binary not (clesperanto) * Tools > Segmentation post-processing > Binary OR / union (clesperanto) * Tools > Segmentation post-processing > Binary subtract (clesperanto) * Tools > Segmentation post-processing > Binary XOR (clesperanto) * Tools > Segmentation post-processing > Exclude large labels (clesperanto) * Tools > Segmentation post-processing > Exclude small labels (clesperanto) * Tools > Segmentation post-processing > Exclude labels with map values out of range (clesperanto) * Tools > Segmentation post-processing > Exclude labels with map values within range (clesperanto) * Tools > Segmentation post-processing > Extend labels via Voronoi (clesperanto) * Tools > Segmentation post-processing > Reduce labels to centroids (clesperanto) * Tools > Segmentation post-processing > Reduce labels to label edges (clesperanto) * Tools > Segmentation post-processing > Dilate Labels (clesperanto) * Tools > Segmentation post-processing > Erode Labels (clesperanto) * Tools > Segmentation post-processing > Opening Labels (clesperanto) * Tools > Segmentation post-processing > Closing Labels (clesperanto)

- Python
Published by haesleinhuepf over 3 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.20.0

New features * Compatibility with morphometrics: label_statistics now show up in morphometrics region properties widget

Backwards compatibility breaking changes: * parameters of the labelstatitstics function were renamed: "image" -> "intensityimage", "labels" -> "label_image"

- Python
Published by haesleinhuepf over 3 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.19.0

New features * Tools > Segmentation post-processing > Merge touching labels (clesperanto) * Tools > Segmentation post-processing > Merge touching labels with intensity along borders within range (clesperanto) * Tools > Segmentation post-processing > Smooth labels (clesperanto)

See also https://github.com/clEsperanto/pyclesperanto_prototype/releases/tag/0.19.0

- Python
Published by haesleinhuepf over 3 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.18.4

New features * Tools > Measurement > Label statistics [of all frames] which includes neighbor statistics * File > Open Samples > clEsperanto > Lung timelapse (100 MB)

Deprecated: * Tools > Measurement > Statistics of labelled pixels [of all frames] * Tools > Measurement > Statistics of labeled pixels including neighborhood statistics [of all frames]

- Python
Published by haesleinhuepf almost 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.18.3

New release to invoke a version bump on conda-forge...

- Python
Published by haesleinhuepf almost 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.18.2

Bug fixes * Select GPU dialog was not working from the plugins menu (thanks to @psobolewskiPhD for reporting)

- Python
Published by haesleinhuepf almost 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.18.1

Bug fix * Generated code didn't work in some cases because two functions were not exposed to the public API

- Python
Published by haesleinhuepf about 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.18.0

Documentation updates * Installation instructions for Mac and Linux were missing an important section (thanks to @marabuuu for reporting the issue)

Backwards compatibility breaking changes * The API of statistics_of_labeled_pixels was modified: * The position of the napari_viewer argument was changed. It is recommended to use it as keyword-argument. * The function now returns Pandas DataFrames instead of a dictionary. * The API of advanced_statistics was modified: * The function now returns Pandas DataFrames instead of a dictionary.

- Python
Published by haesleinhuepf about 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.17.1

New features * Statistics of labeled pixels including distance to neighbors (based on napari-clusters-plotter code by @Cryaaa and @lazigu) * Neighborhood statistics (minimum/mean/median/maximum/standard deviation of measurements of neighboring objects) * New category: Combine labels (via napari-assistant & pyclesperanto-prototype)

Bug fixes * GPU-selector didn't work

Backwards compatibility breacking changes * The clesperanto-based Assistant GUI was removed from the menu. Use Tools > Utilities > Assistant (na) instead

- Python
Published by haesleinhuepf about 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.16.0

New features * Use the napari-assistant as new graphical user interface

Backwards compatibility breaking changes * The Assistant class and related functions have been moved to the napari-assistant repository * statistic_of_labeled_pixels now uses a label image as second parameter and no label-layer anymore * Jython code generation is not available temporarily. Use the python code generator and adapt the code manually in Fiji

- Python
Published by haesleinhuepf about 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.15.5

Bugfix: * divide_image from napari-segment-blobs-and-things-with-membranes caused error when called from the assistant, when only one image was opened (thanks to @Cryaaa for reporting #51 )

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.15.4

Bug fixes * Fixes an issue with XArrays (thanks to @psobolewskiPhD for reporting)

See also https://github.com/clEsperanto/pyclesperanto_prototype/releases/tag/0.15.4

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.15.3

New features * Increased button size (for touch-screen users with thick fingers) * Reduced gap between buttons * Added temporary spinner for tuning button size

Bug fixes * Thanks to multi-line text in combo boxes operation names should now be readable also on Windows

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.15.2

Bugfix * Widgets were requesting too large space (Thanks to @psobolewskiPhD for reporting)

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.15.1

Bugfix * Example data (blobs.tif) wasn't deployed (Thanks to @psobolewskiPhD for reporting)

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.15.0

Bugfixes: * Pulldown entries should be readable again. The width limit was removed

See also https://github.com/clEsperanto/pyclesperantoprototype/blob/master/docs/releasenotes.md#0150---february-12th-2022

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.14.1

Bugfix: * "Filter labels" category didn't result in labels

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.14.0

New features * Save workflow function (thanks to Johannes Müller @jo-mueller and Ryan Savill @Cryaaa) * Better error reporting in case operations fail * New layout (Thanks to Elisabeth Kugler @ElisabethKugler, Kesavan Subburam @pskeshu, Andreas Müller, Michael Morehead @mmorehea and "MadScientist" for constructive feedback via twitter)

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.12.0

Improvements * automated tests * code coverage * better installation instructions

Upstream changes in pyclesperantoprototype: https://github.com/clEsperanto/pyclesperantoprototype/blob/master/docs/release_notes.md#0120---january-1st-2022

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.11.9

Documentation bugfix: * Removed EDAM ontology temporarily as it was spaming the napari hub page

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.11.8

New features * Improved listing in napari hub (thanks to @neuromusic) * Basic compatibility with napari-workflow-optimizer * Store GUI widget in layer.source to improve compatibility with napari

Bug fixes * Fixed future warnings when using the upcoming napari 0.4.13 * Removed a debug trace that was printed when starting up napari

Removed features * Compatibility with napari 0.4.8

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.11.7

New features * Supports listing operations from other plugins that are registered functions in napari-tools-menu * Allow filtering operations using a search-string

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.11.6

New features * Better support for generating workflows using napari-time-slicer / napari-workflow-inspector. The assistant notifies the workflow manager now if it does something and the workflow manager records it properly, allowing code generation from the workflow inspector.

See also https://github.com/clEsperanto/pyclesperantoprototype/blob/master/docs/releasenotes.md#0112---december-5th-2021

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.11.5

Backwards compatible changes * Changed menu entries to cover finer differentiation between various filtering and segmentation techniquese

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.11.4

Bugfixes * Deployment: Too large wheels/files were packed

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.11.3

Bug fixes * contrast_limits were not in generated code

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.11.2

Bugfix * Generated code didn't work properly in 3D cases

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.11.1

New features * Integration of the napari-script-editor for easier script generation * The "Measure" button is back to the Assistant user interface giving easier access to tabular results data

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.11.0

New features * optional cupy backend in pyclesperanto-prototype 0.11.0 (read more) * use table from napari-skimage-regionprops for showing statistical measurements

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.10.10

New features * Connected Component labeling in the Tools > Segmentation menu * Voronoi-Otsu-labeling in the Tools > Segmentation menu * Use the time-slicer for these two new function when processing timelapse data

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.10.9

Bug fixes * Copying and saving tables did't work (Thanks to Laura Žigutytė @lazigu for reporting)

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.10.8

Bugfix: * Removed dyfunctional operations from the "Label processing" category

See also: https://github.com/clEsperanto/pyclesperantoprototype/blob/master/docs/releasenotes.md#0108

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.10.7

New features * New category: "Compare label images" * Example data is now longer distributed, it's downloaded from the internet (except blobs)

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.10.6

New features * Statistics of labeled pixels in Tools menu * Interactive table like in napari-skimage-regionprops * Added split-stack to Tools menu

Bugfix: * Statistics table was freezing napari

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.10.4

Update release due to upstream bugfix: https://github.com/clEsperanto/pyclesperantoprototype/blob/master/docs/releasenotes.md#0104---october-26th-2021

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.10.3

Bug fixes * Installation issues on MacOS (Thanks to Kevin Yamauchi @kevinyamauchi for the PR!) * After removing layers, sometimes they reappeared

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.10.2

New features * Added entries to Tools menu

Bug fixes: * Reset brightness/contrast didn't work on dask-backed image layers

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.10.1

New features: * DOI generation for releases on zenodo.org

- Python
Published by haesleinhuepf over 4 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.10.0

New features: * Example data: blobs from ImageJ 🥳 * GPU-backed label images can now be modified interactively in napari

See also https://github.com/clEsperanto/pyclesperanto_prototype/releases/tag/0.10.0

- Python
Published by haesleinhuepf almost 5 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.9.10

Bugfix: * Revert to former menu structure to fix lost menus

- Python
Published by haesleinhuepf almost 5 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.9.9

New Features * Reorganized menu: Categories of "What" you can do are primary focus. * Utilitiy function for converting label layers to images and images to label layers

See also https://github.com/clEsperanto/pyclesperantoprototype/blob/master/docs/releasenotes.md#099---august-1st-2021

- Python
Published by haesleinhuepf almost 5 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.9.8

Bug fixes: * Right-click on operation pull-down made napari freeze

Miscellaneous * Improved installation instructions for Windows. No command line needed anymore

See also: * https://github.com/clEsperanto/pyclesperantoprototype/blob/master/docs/releasenotes.md#097---july-15th-2021

- Python
Published by haesleinhuepf almost 5 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.9.6

Bugfixes: * The execution-order of chained operations was interrupted when the user changed the input-image of an operation. * The help-button was sometimes above the whole user interface. It was removed. You find the online help by right-clicking on the operations-pulldown instead.

- Python
Published by haesleinhuepf almost 5 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.9.5

New Features * Help button in image processing operations * Tooltips for categories give short description * Tooltips showing short documentation for processing steps * Grid order in napari now goes from top-left to bottom-right showing intermediate processing results * New convenience functions in menu Plugins > clEsperanto * Make labels editable * Auto brightness contrast * Auto brightness contrast of all images * Reset brightness contrast * Split stack (e.g. for splitting channels) * Set voxel size * Set voxel size of all images * Voxel size is propagated from stack to stack when adding processing steps * Added example dataset "HaaseMRTtfl3d1" loaded from Zenodo

Removed features * Auto-contrast when updating operation parameters

Bug fixes * Code generators now contain the loaded image filename of the source image * Projections crashed napari when selecting the category

See also changes in pyclesperanto 0.9.5: * https://github.com/clEsperanto/pyclesperantoprototype/blob/master/docs/releasenotes.md#095---july-11th-2021

- Python
Published by haesleinhuepf almost 5 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.9.4

New features: * Select-GPU dialog when starting the Assistant * Support for 4D-data by processing 3D stacks individually and updating when the user changes the time point slider * Function for turing a 3D image into a 2D+t stack * Renamed categories, e.g. "Background removal" -> "Remove background" * Reorganized categories: Better differentiation between label neighbor filters, label measurements and label-image measurements

See also * https://github.com/clEsperanto/pyclesperantoprototype/blob/master/docs/releasenotes.md#094---july-3rd-2021

- Python
Published by haesleinhuepf almost 5 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.9.2

See also https://github.com/clEsperanto/pyclesperantoprototype/blob/master/docs/releasenotes.md#092---june-26th-2021

- Python
Published by haesleinhuepf almost 5 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.9.0

New features * User interface for measuring label statistics (in the menu)

See also: * https://github.com/clEsperanto/pyclesperantoprototype/blob/master/docs/releasenotes.md#090---may-16th-2021

- Python
Published by haesleinhuepf about 5 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.8.0

New features * Show multiple dock widgets in napari 0.4.8 * Moved menu entries to buttons in the assistant widget * Use dask under the hood to manage execution order of operations * New and more flexible user interfaces for the button grid * Push/pull images to/from GPU memory were minimized bringing improved performance, napari can have OCLArrays as layers since pyclesperanto 0.8.0

Bug fixes * Operations are no longer executed twice when added * Some categories didn't show all parameters which were needed to configure the operations

Backwards compatiblity breaking changes * Improved, simplified and easier extensible backend for categories * New code generators based on jupytext

Special big thanks to Talley Lambert who made most of these!

- Python
Published by haesleinhuepf about 5 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.7.6

Bug fixes * The user interface was confused when multiple operations of the same kind were executed. Thus, better handling of stateful operations attached to layers was implemented. Big thanks to Talley Lambert for suggesting how to fix that.

Miscellaneous * A test was added to simulate a complex workflow executed in the CI.

- Python
Published by haesleinhuepf about 5 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.7.5

New features * Added new operation categories: transforms and projections * Layerdialogs now adapt parameter labels depending on which operation is chosen

See also: https://github.com/clEsperanto/pyclesperanto_prototype/releases/tag/0.7.5

- Python
Published by haesleinhuepf about 5 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.7.4 (alpha)

This pre-release updates dependencies to napari 0.4.7

- Python
Published by haesleinhuepf about 5 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.7.3 (alpha)

This comes with pyclesperantoprototype 0.7.3 https://github.com/clEsperanto/pyclesperantoprototype/releases/tag/0.7.3

Known issues * This release is not compatible with napari 0.4.7 and magicgui 0.2.7. Use napari 0.4.5 and magicgui 0.2.5 instead.

- Python
Published by haesleinhuepf about 5 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.7.2

This pre-release updates dependencies to * napari 0.4.5 and * magicgui 0.2.6

- Python
Published by haesleinhuepf over 5 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.7.1

Bugfix: button icons were not deployed

- Python
Published by haesleinhuepf over 5 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.7.0

This comes with napari release 0.4.3 and pyclesperanto 0.7.0

See https://github.com/napari/napari/releases/tag/v0.4.3 https://github.com/clEsperanto/pyclesperantoprototype/blob/master/docs/releasenotes.md

- Python
Published by haesleinhuepf over 5 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.2.1

New features * Export Jython/Python code to clipboard menu

Bug fixes: * Generated code contained some duplicates of operations in case operations from category 'combine' were used. * Prevent printing out images as text in notebooks * Notebooks visualize maximum-z-projections of 3D images instead of crashing

- Python
Published by haesleinhuepf over 5 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.2.0 (alpha)

New features * Syncronized Jython with Python Code generation, ensured compatiblity with the Java side * GUI improvement such as more stable dock widget size * Improved layer naming to prevent mixing up images and operations in GUI

See also: https://github.com/clEsperanto/pyclesperantoprototype/blob/master/docs/releasenotes.md

- Python
Published by haesleinhuepf over 5 years ago

https://github.com/clesperanto/napari_pyclesperanto_assistant - 0.1.0

First pre-release to see if deployment works

- Python
Published by haesleinhuepf over 5 years ago