Recent Releases of ilastik

ilastik - 1.4.1.post1

Fix license/third-party licence dialog.

Full Changelog: https://github.com/ilastik/ilastik/compare/1.4.1...1.4.1.post1

- Python
Published by k-dominik 9 months ago

What's Changed

Summary:

Support for OME-zarr (v0.4) details in our documentation
New workflow - Trainable Domain Adaptation
New object features based on Spherical Harmonics Feature Extraction contributed by @oanegros
Native support for Apple Silicon (M1, M2, M3, M4)

Full list of pull requests

* fix elf ws now returns uint64 by @k-dominik in https://github.com/ilastik/ilastik/pull/2690 * mnt: update pytorch versions by @k-dominik in https://github.com/ilastik/ilastik/pull/2692 * mnt: wsdt package not used by @k-dominik in https://github.com/ilastik/ilastik/pull/2685 * functionality to ignore multiple dirty propagations from same source by @k-dominik in https://github.com/ilastik/ilastik/pull/2694 * release pin on pytest by @k-dominik in https://github.com/ilastik/ilastik/pull/2633 * Add Trainable Domain Adaptation workflow by @k-dominik in https://github.com/ilastik/ilastik/pull/2704 * Rearrange labeling UI by @btbest in https://github.com/ilastik/ilastik/pull/2705 * fix tda export names by @k-dominik in https://github.com/ilastik/ilastik/pull/2708 * Restyle label table by @btbest in https://github.com/ilastik/ilastik/pull/2710 * bump python version by @k-dominik in https://github.com/ilastik/ilastik/pull/2703 * Osx arm 64 by @k-dominik in https://github.com/ilastik/ilastik/pull/2709 * increase timeout to launch tiktorch by @k-dominik in https://github.com/ilastik/ilastik/pull/2720 * Fix conservation tracking tests by @btbest in https://github.com/ilastik/ilastik/pull/2716 * unfreeze cache before exporting data from tda workflow by @k-dominik in https://github.com/ilastik/ilastik/pull/2723 * hacky fix for elf limiting threads by @k-dominik in https://github.com/ilastik/ilastik/pull/2724 * fix test mouse move by @k-dominik in https://github.com/ilastik/ilastik/pull/2736 * make NN-related operators aware of tensor ids by @k-dominik in https://github.com/ilastik/ilastik/pull/2732 * replace vigra for tiff reading with tifffile by @k-dominik in https://github.com/ilastik/ilastik/pull/2733 * bigger shape in 'z' for tiffs means faster browsing by @k-dominik in https://github.com/ilastik/ilastik/pull/2737 * Fix devenv by @k-dominik in https://github.com/ilastik/ilastik/pull/2726 * Disabled addRemoveData test by @k-dominik in https://github.com/ilastik/ilastik/pull/2742 * Undo elf fix by @k-dominik in https://github.com/ilastik/ilastik/pull/2734 * Data input: Phrase axistags error message more user-friendly by @btbest in https://github.com/ilastik/ilastik/pull/2747 * First try most compatible H5 saving, otherwise use v1.8 by @oanegros in https://github.com/ilastik/ilastik/pull/2746 * reduce number of deprecation warnings by @k-dominik in https://github.com/ilastik/ilastik/pull/2740 * Bump akaihola/darker from 1.6.0 to 1.7.2 by @dependabot in https://github.com/ilastik/ilastik/pull/2753 * Bump actions/checkout from 2 to 4 by @dependabot in https://github.com/ilastik/ilastik/pull/2754 * Request object features per plugin in parallel by @k-dominik in https://github.com/ilastik/ilastik/pull/2750 * experimental API refactor by @k-dominik in https://github.com/ilastik/ilastik/pull/2752 * OpDataSelection: Directly obtain data-reader by @btbest in https://github.com/ilastik/ilastik/pull/2757 * Remove string concatenation when raising by @btbest in https://github.com/ilastik/ilastik/pull/2759 * bump tiktorch by @k-dominik in https://github.com/ilastik/ilastik/pull/2765 * also exclude broken xarray version in conda pkg by @k-dominik in https://github.com/ilastik/ilastik/pull/2768 * exclude broken xarray builds by @k-dominik in https://github.com/ilastik/ilastik/pull/2769 * lazyflow: use exception chaining in requests by @k-dominik in https://github.com/ilastik/ilastik/pull/2760 * Remove obsolete OpTransposeSlots by @btbest in https://github.com/ilastik/ilastik/pull/2762 * OpDataSelection: Default file exports to project file path by @btbest in https://github.com/ilastik/ilastik/pull/2774 * bump numpy 1.22 by @k-dominik in https://github.com/ilastik/ilastik/pull/2775 * try larger resource class for tests on circleci by @k-dominik in https://github.com/ilastik/ilastik/pull/2767 * Bump conda-incubator/setup-miniconda from 2 to 3 by @dependabot in https://github.com/ilastik/ilastik/pull/2780 * Multiscale v1 by @btbest in https://github.com/ilastik/ilastik/pull/2782 * Object size filter: Increase permitted value range by @btbest in https://github.com/ilastik/ilastik/pull/2784 * fixed `skimage.segmentation.slic` signature change by @k-dominik in https://github.com/ilastik/ilastik/pull/2792 * Prettify dataset table by @btbest in https://github.com/ilastik/ilastik/pull/2793 * Labeling GUI: Copy colortable by @btbest in https://github.com/ilastik/ilastik/pull/2786 * remove OpBigTiffReader by @k-dominik in https://github.com/ilastik/ilastik/pull/2799 * better "debug" for error in command line usage by @k-dominik in https://github.com/ilastik/ilastik/pull/2763 * Bump actions/cache from 3 to 4 by @dependabot in https://github.com/ilastik/ilastik/pull/2802 * Tests: Fix mock table and assert combobox attempts to change by @btbest in https://github.com/ilastik/ilastik/pull/2804 * Reimplement urldatasetinfo as legacy by @btbest in https://github.com/ilastik/ilastik/pull/2805 * Fix pytest8 by @btbest in https://github.com/ilastik/ilastik/pull/2808 * Tests: Deflake scale combobox in test on MacOS by @btbest in https://github.com/ilastik/ilastik/pull/2806 * Bump al-cheb/configure-pagefile-action from 1.3 to 1.4 by @dependabot in https://github.com/ilastik/ilastik/pull/2809 * Use key-strings to identify multiscales by @btbest in https://github.com/ilastik/ilastik/pull/2801 * Change default export format to compressed hdf5 by @k-dominik in https://github.com/ilastik/ilastik/pull/2812 * Multiscale: Support project files containing an integer working_scale by @btbest in https://github.com/ilastik/ilastik/pull/2816 * Data Export: Update buttons after removing lane by @btbest in https://github.com/ilastik/ilastik/pull/2815 * ci: circumvent disk space limitation on D: by @k-dominik in https://github.com/ilastik/ilastik/pull/2817 * Fixed OpMultiChannelSelector by @k-dominik in https://github.com/ilastik/ilastik/pull/2748 * let pytest use pytest.ini to discover tests by @k-dominik in https://github.com/ilastik/ilastik/pull/2745 * Tests: Mock user interaction in ImageFileDialog by @btbest in https://github.com/ilastik/ilastik/pull/2819 * Ensure all object features get exported to table by @k-dominik in https://github.com/ilastik/ilastik/pull/2814 * Data selection: Remove inline Add buttons immediately by @btbest in https://github.com/ilastik/ilastik/pull/2821 * Added note that data is copied to project file by @k-dominik in https://github.com/ilastik/ilastik/pull/2818 * Improve web loading gui by @btbest in https://github.com/ilastik/ilastik/pull/2820 * Multiscale: Save scale by @btbest in https://github.com/ilastik/ilastik/pull/2826 * Bump akaihola/darker from 1.7.2 to 1.7.3 by @dependabot in https://github.com/ilastik/ilastik/pull/2829 * Bump akaihola/darker from 1.7.3 to 2.0.0 by @dependabot in https://github.com/ilastik/ilastik/pull/2833 * Bump akaihola/darker from 2.0.0 to 2.1.0 by @dependabot in https://github.com/ilastik/ilastik/pull/2835 * Fix layerviewer update after shape change by @btbest in https://github.com/ilastik/ilastik/pull/2831 * Precomputed handling by @btbest in https://github.com/ilastik/ilastik/pull/2832 * Multi-GUI adapter: Stop throwing if no lanes exist by @btbest in https://github.com/ilastik/ilastik/pull/2837 * Refactor applet serializer by @k-dominik in https://github.com/ilastik/ilastik/pull/2838 * Feature selection: Stop throwing if no lanes exist by @btbest in https://github.com/ilastik/ilastik/pull/2839 * Debug logging by @btbest in https://github.com/ilastik/ilastik/pull/2841 * Update open recent project list when saving as a project by @thodkatz in https://github.com/ilastik/ilastik/pull/2842 * Add note on 'bad features' warning for skewness and kurtosis by @k-dominik in https://github.com/ilastik/ilastik/pull/2847 * Remove transaction by @btbest in https://github.com/ilastik/ilastik/pull/2848 * Bump akaihola/darker from 2.1.0 to 2.1.1 by @dependabot in https://github.com/ilastik/ilastik/pull/2849 * Update classifier serialization by @k-dominik in https://github.com/ilastik/ilastik/pull/2840 * Python 3.10 compatiblity fixes by @k-dominik in https://github.com/ilastik/ilastik/pull/2856 * Web-loading GUI: Update OK button by @btbest in https://github.com/ilastik/ilastik/pull/2851 * Delay setupLayers to LayerGui being shown by @k-dominik in https://github.com/ilastik/ilastik/pull/2858 * Use pydantic for .ilp deserialization in experimental/api by @k-dominik in https://github.com/ilastik/ilastik/pull/2846 * Fix image links in api test projects by @k-dominik in https://github.com/ilastik/ilastik/pull/2859 * Add experimental autocontext api by @k-dominik in https://github.com/ilastik/ilastik/pull/2857 * Lazyflow logging and fix default operator naming by @btbest in https://github.com/ilastik/ilastik/pull/2850 * omg Zarr by @btbest in https://github.com/ilastik/ilastik/pull/2862 * Fix circleci by @k-dominik in https://github.com/ilastik/ilastik/pull/2876 * Start QApplication with non-empty argv by @k-dominik in https://github.com/ilastik/ilastik/pull/2873 * Fix circleCI pt2: try to get pytest output immediately by @k-dominik in https://github.com/ilastik/ilastik/pull/2878 * Oc plugins via entrypoints by @k-dominik in https://github.com/ilastik/ilastik/pull/2875 * Fixes for 1.4.1b17 release by @btbest in https://github.com/ilastik/ilastik/pull/2883 * Pixel Classification: Fix pop error by @btbest in https://github.com/ilastik/ilastik/pull/2889 * Add sphericaltexture_plugin to default object feature plugins by @k-dominik in https://github.com/ilastik/ilastik/pull/2890 * Object classification: Restore default feature selection from previous verisons by @k-dominik in https://github.com/ilastik/ilastik/pull/2892 * Skip requestLock test on CircleCI by @btbest in https://github.com/ilastik/ilastik/pull/2880 * Easier problem reporting by @btbest in https://github.com/ilastik/ilastik/pull/2879 * Add wait cursor when tiktorch server is started by @thodkatz in https://github.com/ilastik/ilastik/pull/2882 * H5N5 writing: Refactor test - readability, disentangle test cases by @btbest in https://github.com/ilastik/ilastik/pull/2896 * Autocontext: Connect raw data directly in 2nd (or later) rounds by @k-dominik in https://github.com/ilastik/ilastik/pull/2866 * Fix dark mode (for mac) by @k-dominik in https://github.com/ilastik/ilastik/pull/2898 * remove all things related to ipc by @k-dominik in https://github.com/ilastik/ilastik/pull/2900 * remove hbp-related project upload functionality by @k-dominik in https://github.com/ilastik/ilastik/pull/2901 * OME-Zarr in headless and API by @btbest in https://github.com/ilastik/ilastik/pull/2895 * Stop using mamba by @btbest in https://github.com/ilastik/ilastik/pull/2904 * Fix typo in carve/preprocessing by @j6k4m8 in https://github.com/ilastik/ilastik/pull/2908 * update pin for tiktorch by @k-dominik in https://github.com/ilastik/ilastik/pull/2910 * Fix flaky ObjectClassificationGui test by @k-dominik in https://github.com/ilastik/ilastik/pull/2911 * remove faulthandler activation on lazyflow import by @k-dominik in https://github.com/ilastik/ilastik/pull/2914 * Removed unused `SerialHdf5BlockSlot` by @k-dominik in https://github.com/ilastik/ilastik/pull/2915 * Export to OME-Zarr by @btbest in https://github.com/ilastik/ilastik/pull/2907 * OME-Zarr export: Fix export when source dataset is OME-Zarr v0.1 by @btbest in https://github.com/ilastik/ilastik/pull/2924 * Fix pytorch fbgemm.dll dependency issue by @btbest in https://github.com/ilastik/ilastik/pull/2927 * Multiscale: Preview scale file size in dropdown by @btbest in https://github.com/ilastik/ilastik/pull/2923 * Add logging widget to status bar by @k-dominik in https://github.com/ilastik/ilastik/pull/2928 * Support selecting/loading arbitrary URIs within an OME-Zarr store by @btbest in https://github.com/ilastik/ilastik/pull/2897 * Update ilastik with the new bioimageio v0.5 spec by @thodkatz in https://github.com/ilastik/ilastik/pull/2919 * Multicut: Fix deprecated append on pd.DataFrame by @k-dominik in https://github.com/ilastik/ilastik/pull/2934 * Switch to .conda package format (with latest conda build) by @k-dominik in https://github.com/ilastik/ilastik/pull/2935 * Tests: disable automatic cache cleanup for lazyflow tests. by @k-dominik in https://github.com/ilastik/ilastik/pull/2938 * Fix persisting NotificationsWindow during test runs by @k-dominik in https://github.com/ilastik/ilastik/pull/2937 * OME-Zarr: Report v0.5 not supported by @btbest in https://github.com/ilastik/ilastik/pull/2939 * bump vigra to 1.11.1 build 1038 by @k-dominik in https://github.com/ilastik/ilastik/pull/2941 * Carving: Disable mesh export for 2D and improve responsiveness by @btbest in https://github.com/ilastik/ilastik/pull/2912 * OME-Zarr: Support reading from URIs with s3: scheme by @btbest in https://github.com/ilastik/ilastik/pull/2940 * Fix state update to inactivate applets in live update by @k-dominik in https://github.com/ilastik/ilastik/pull/2902 * Added drag-n-drop support for projects to startup page by @k-dominik in https://github.com/ilastik/ilastik/pull/2948 * Error on missing plugin by @k-dominik in https://github.com/ilastik/ilastik/pull/2945 * OC: Change default table export format to csv by @k-dominik in https://github.com/ilastik/ilastik/pull/2947 * OC: Add undo/redo for object level annotations by @k-dominik in https://github.com/ilastik/ilastik/pull/2949 * Better recovery from batch processing failures by @k-dominik in https://github.com/ilastik/ilastik/pull/2946 * Fix tracking export plugins by @k-dominik in https://github.com/ilastik/ilastik/pull/2943 * Unpin grpcio, devenv uses 1.49 already by @k-dominik in https://github.com/ilastik/ilastik/pull/2952 * Quickfix: Same object size limits in tracking and oc by @k-dominik in https://github.com/ilastik/ilastik/pull/2958 * OME-Zarr: Sync front- and backend check for compatibility by @btbest in https://github.com/ilastik/ilastik/pull/2956 * Tda UI improvements by @k-dominik in https://github.com/ilastik/ilastik/pull/2950 * Add 2d_cells zarr as default in Multiscale history by @k-dominik in https://github.com/ilastik/ilastik/pull/2957 * Fix show model name for models from ilp by @k-dominik in https://github.com/ilastik/ilastik/pull/2960 * Add cpu fallback for tiktorch server on macos silicon by @k-dominik in https://github.com/ilastik/ilastik/pull/2961 * Add deprecation notice for PC+OC workflow by @k-dominik in https://github.com/ilastik/ilastik/pull/2962 * Fix spelling errors and improve documentation by @AryanK37 in https://github.com/ilastik/ilastik/pull/2964 * Fix: forgot to add tda without beta to list of workflows :[ by @k-dominik in https://github.com/ilastik/ilastik/pull/2963 * Filter out unsupported extensions by @AryanK37 in https://github.com/ilastik/ilastik/pull/2965 * Removed spelling errors by @Palak1725 in https://github.com/ilastik/ilastik/pull/2966 * Fix documentation typos by @tanishac25 in https://github.com/ilastik/ilastik/pull/2980 * Add `DatasetOut` slot to OpDataSelection, Fix segfaults by @k-dominik in https://github.com/ilastik/ilastik/pull/2968 * DataSelection don't show viewer for every added file by @k-dominik in https://github.com/ilastik/ilastik/pull/2991 * Optimize bioimage model downloads, update tiktoch/bioimageio by @k-dominik in https://github.com/ilastik/ilastik/pull/2974 * 1.4.1 prep by @k-dominik in https://github.com/ilastik/ilastik/pull/2993 * Fix circleci build by @k-dominik in https://github.com/ilastik/ilastik/pull/3005 * Really last changes before release by @k-dominik in https://github.com/ilastik/ilastik/pull/3006 * Fix relative logfile path handling by @emilmelnikov in https://github.com/ilastik/ilastik/pull/3008 * Fix dependency conflicts with boa, and go back to conda build by @k-dominik in https://github.com/ilastik/ilastik/pull/3012

New Contributors

We would like to thank everyone who did their first contribution to ilastik!

@oanegros made their first contribution in https://github.com/ilastik/ilastik/pull/2746
@thodkatz made their first contribution in https://github.com/ilastik/ilastik/pull/2842
@j6k4m8 made their first contribution in https://github.com/ilastik/ilastik/pull/2908
@AryanK37 made their first contribution in https://github.com/ilastik/ilastik/pull/2964
@Palak1725 made their first contribution in https://github.com/ilastik/ilastik/pull/2966
@tanishac25 made their first contribution in https://github.com/ilastik/ilastik/pull/2980

Full Changelog: https://github.com/ilastik/ilastik/compare/1.4.0...1.4.1

- Python
Published by k-dominik 10 months ago

ilastik - 1.4.1rc2

What's Changed

Switch to .conda package format (with latest conda build) by @k-dominik in https://github.com/ilastik/ilastik/pull/2935
Tests: disable automatic cache cleanup for lazyflow tests. by @k-dominik in https://github.com/ilastik/ilastik/pull/2938
Fix persisting NotificationsWindow during test runs by @k-dominik in https://github.com/ilastik/ilastik/pull/2937
OME-Zarr: Report v0.5 not supported by @btbest in https://github.com/ilastik/ilastik/pull/2939
bump vigra to 1.11.1 build 1038 by @k-dominik in https://github.com/ilastik/ilastik/pull/2941
Carving: Disable mesh export for 2D and improve responsiveness by @btbest in https://github.com/ilastik/ilastik/pull/2912
OME-Zarr: Support reading from URIs with s3: scheme by @btbest in https://github.com/ilastik/ilastik/pull/2940
Fix state update to inactivate applets in live update by @k-dominik in https://github.com/ilastik/ilastik/pull/2902
Added drag-n-drop support for projects to startup page by @k-dominik in https://github.com/ilastik/ilastik/pull/2948
Error on missing plugin by @k-dominik in https://github.com/ilastik/ilastik/pull/2945
OC: Change default table export format to csv by @k-dominik in https://github.com/ilastik/ilastik/pull/2947
OC: Add undo/redo for object level annotations by @k-dominik in https://github.com/ilastik/ilastik/pull/2949
Better recovery from batch processing failures by @k-dominik in https://github.com/ilastik/ilastik/pull/2946
Fix tracking export plugins by @k-dominik in https://github.com/ilastik/ilastik/pull/2943
Unpin grpcio, devenv uses 1.49 already by @k-dominik in https://github.com/ilastik/ilastik/pull/2952

Full Changelog: https://github.com/ilastik/ilastik/compare/1.4.1b23...1.4.1rc2

- Python
Published by k-dominik 12 months ago

ilastik - 1.4.1b23

What's Changed

OME-Zarr export: Fix export when source dataset is OME-Zarr v0.1 by @btbest in https://github.com/ilastik/ilastik/pull/2924
Fix pytorch fbgemm.dll dependency issue by @btbest in https://github.com/ilastik/ilastik/pull/2927
Multiscale: Preview scale file size in dropdown by @btbest in https://github.com/ilastik/ilastik/pull/2923
Add logging widget to status bar by @k-dominik in https://github.com/ilastik/ilastik/pull/2928
Support selecting/loading arbitrary URIs within an OME-Zarr store by @btbest in https://github.com/ilastik/ilastik/pull/2897
Update ilastik with the new bioimageio v0.5 spec by @thodkatz in https://github.com/ilastik/ilastik/pull/2919
Multicut: Fix deprecated append on pd.DataFrame by @k-dominik in https://github.com/ilastik/ilastik/pull/2934

Full Changelog: https://github.com/ilastik/ilastik/compare/1.4.1b22...1.4.1b23

- Python
Published by k-dominik about 1 year ago

ilastik - 1.4.1b22

What's Changed

Removed unused SerialHdf5BlockSlot by @k-dominik in https://github.com/ilastik/ilastik/pull/2915
Export to OME-Zarr by @btbest in https://github.com/ilastik/ilastik/pull/2907

Full Changelog: https://github.com/ilastik/ilastik/compare/1.4.1b21...1.4.1b22

- Python
Published by btbest over 1 year ago

ilastik - 1.4.1b21

What's Changed

Skip requestLock test on CircleCI by @btbest in https://github.com/ilastik/ilastik/pull/2880
Easier problem reporting by @btbest in https://github.com/ilastik/ilastik/pull/2879
Add wait cursor when tiktorch server is started by @thodkatz in https://github.com/ilastik/ilastik/pull/2882
H5N5 writing: Refactor test - readability, disentangle test cases by @btbest in https://github.com/ilastik/ilastik/pull/2896
Autocontext: Connect raw data directly in 2nd (or later) rounds by @k-dominik in https://github.com/ilastik/ilastik/pull/2866
Fix dark mode (for mac) by @k-dominik in https://github.com/ilastik/ilastik/pull/2898
remove all things related to ipc by @k-dominik in https://github.com/ilastik/ilastik/pull/2900
remove hbp-related project upload functionality by @k-dominik in https://github.com/ilastik/ilastik/pull/2901
OME-Zarr in headless and API by @btbest in https://github.com/ilastik/ilastik/pull/2895
Stop using mamba by @btbest in https://github.com/ilastik/ilastik/pull/2904
Fix typo in carve/preprocessing by @j6k4m8 in https://github.com/ilastik/ilastik/pull/2908
update pin for tiktorch by @k-dominik in https://github.com/ilastik/ilastik/pull/2910
Fix flaky ObjectClassificationGui test by @k-dominik in https://github.com/ilastik/ilastik/pull/2911
remove faulthandler activation on lazyflow import by @k-dominik in https://github.com/ilastik/ilastik/pull/2914

New Contributors

@j6k4m8 made their first contribution in https://github.com/ilastik/ilastik/pull/2908

Full Changelog: https://github.com/ilastik/ilastik/compare/1.4.1b20...1.4.1b21

- Python
Published by k-dominik over 1 year ago

ilastik - 1.4.1b20

What's Changed

Pixel Classification: Fix pop error by @btbest in https://github.com/ilastik/ilastik/pull/2889
Add sphericaltexture_plugin to default object feature plugins by @oanegros in https://github.com/ilastik/ilastik/pull/2890 (preprint)
Object classification: Restore default feature selection from previous verisons by @k-dominik in https://github.com/ilastik/ilastik/pull/2892

Full Changelog: https://github.com/ilastik/ilastik/compare/1.4.1b18...1.4.1b20

- Python
Published by k-dominik over 1 year ago

ilastik - 1.4.1b18

What's Changed

Fix layerviewer update after shape change by @btbest in https://github.com/ilastik/ilastik/pull/2831
Delay setupLayers to LayerGui being shown by @k-dominik in https://github.com/ilastik/ilastik/pull/2858
Multi-GUI adapter/Feature selection: Stop throwing if no lanes exist by @btbest in https://github.com/ilastik/ilastik/pull/2837 / https://github.com/ilastik/ilastik/pull/2839
Refactor applet serializer by @k-dominik in https://github.com/ilastik/ilastik/pull/2838
Update open recent project list when saving as a project by @thodkatz in https://github.com/ilastik/ilastik/pull/2842
Add note on 'bad features' warning for skewness and kurtosis by @k-dominik in https://github.com/ilastik/ilastik/pull/2847
Update classifier serialization by @k-dominik in https://github.com/ilastik/ilastik/pull/2840
Python 3.10 compatiblity fixes by @k-dominik in https://github.com/ilastik/ilastik/pull/2856
Use pydantic for .ilp deserialization in experimental/api by @k-dominik in https://github.com/ilastik/ilastik/pull/2846
Fix image links in api test projects by @k-dominik in https://github.com/ilastik/ilastik/pull/2859
Add experimental autocontext api by @k-dominik in https://github.com/ilastik/ilastik/pull/2857
Lazyflow logging and fix default operator naming by @btbest in https://github.com/ilastik/ilastik/pull/2850
Minor Precomputed handling improvements by @btbest in https://github.com/ilastik/ilastik/pull/2832
omg Zarr by @btbest in https://github.com/ilastik/ilastik/pull/2862
Start QApplication with non-empty argv by @k-dominik in https://github.com/ilastik/ilastik/pull/2873
Object classification plugins via entrypoints by @k-dominik in https://github.com/ilastik/ilastik/pull/2875

New Contributors

@thodkatz made their first contribution in https://github.com/ilastik/ilastik/pull/2842 🎉🚀

Full Changelog: https://github.com/ilastik/ilastik/compare/1.4.1b15...1.4.1b18

- Python
Published by btbest over 1 year ago

ilastik - ilastik 1.4.1b15

Summary

Future-proofing and backwards compatibility of the Precomputed implementation
UX improvements in data selection and object classification
Default export in compressed hdf5

What's Changed

Object size filter: Increase permitted value range by @btbest in https://github.com/ilastik/ilastik/pull/2784
fixed skimage.segmentation.slic signature change by @k-dominik in https://github.com/ilastik/ilastik/pull/2792
Prettify dataset table by @btbest in https://github.com/ilastik/ilastik/pull/2793
Labeling GUI: Copy colortable by @btbest in https://github.com/ilastik/ilastik/pull/2786
remove OpBigTiffReader by @k-dominik in https://github.com/ilastik/ilastik/pull/2799
better "debug" for error in command line usage by @k-dominik in https://github.com/ilastik/ilastik/pull/2763
Reimplement urldatasetinfo as legacy by @btbest in https://github.com/ilastik/ilastik/pull/2805
Use key-strings to identify multiscales by @btbest in https://github.com/ilastik/ilastik/pull/2801
Change default export format to compressed hdf5 by @k-dominik in https://github.com/ilastik/ilastik/pull/2812
Multiscale: Support project files containing an integer working_scale by @btbest in https://github.com/ilastik/ilastik/pull/2816
Data Export: Update buttons after removing lane by @btbest in https://github.com/ilastik/ilastik/pull/2815
Fixed OpMultiChannelSelector by @k-dominik in https://github.com/ilastik/ilastik/pull/2748
Ensure all object features get exported to table by @k-dominik in https://github.com/ilastik/ilastik/pull/2814
Data selection: Remove inline Add buttons immediately by @btbest in https://github.com/ilastik/ilastik/pull/2821
Added note that data is copied to project file by @k-dominik in https://github.com/ilastik/ilastik/pull/2818
Improve web loading gui by @btbest in https://github.com/ilastik/ilastik/pull/2820
Multiscale: Save scale by @btbest in https://github.com/ilastik/ilastik/pull/2826
ci: circumvent disk space limitation on D: by @k-dominik in https://github.com/ilastik/ilastik/pull/2817
let pytest use pytest.ini to discover tests by @k-dominik in https://github.com/ilastik/ilastik/pull/2745
Fix pytest8 by @btbest in https://github.com/ilastik/ilastik/pull/2808
Tests: Deflake scale combobox in test on MacOS by @btbest in https://github.com/ilastik/ilastik/pull/2806
Tests: Mock user interaction in ImageFileDialog by @btbest in https://github.com/ilastik/ilastik/pull/2819
Tests: Fix mock table and assert combobox attempts to change by @btbest in https://github.com/ilastik/ilastik/pull/2804

Full Changelog: https://github.com/ilastik/ilastik/compare/1.4.1b13...1.4.1b15

- Python
Published by btbest almost 2 years ago

ilastik - ilastik 1.4.1b13

Summary

Simple multiscale support for remote datasets in Neuroglancer Precomputed format.

What's Changed

lazyflow: use exception chaining in requests by @k-dominik in https://github.com/ilastik/ilastik/pull/2760
Remove obsolete OpTransposeSlots by @btbest in https://github.com/ilastik/ilastik/pull/2762
OpDataSelection: Default file exports to project file path by @btbest in https://github.com/ilastik/ilastik/pull/2774
bump numpy 1.22 by @k-dominik in https://github.com/ilastik/ilastik/pull/2775
try larger resource class for tests on circleci by @k-dominik in https://github.com/ilastik/ilastik/pull/2767
Bump conda-incubator/setup-miniconda from 2 to 3 by @dependabot in https://github.com/ilastik/ilastik/pull/2780
Multiscale v1 by @btbest in https://github.com/ilastik/ilastik/pull/2782

Full Changelog: https://github.com/ilastik/ilastik/compare/1.4.1b10...1.4.1b13

- Python
Published by btbest about 2 years ago

ilastik - ilastik 1.4.1b10

fixed incompatible xarray versions that led to failures in the Neural Network workflow.

- Python
Published by k-dominik over 2 years ago

ilastik - 1.4.1b9

Summary

fix neural network workflow with updated zenodo api

What's Changed

OpDataSelection: Directly obtain data-reader by @btbest in https://github.com/ilastik/ilastik/pull/2757
Remove string concatenation when raising by @btbest in https://github.com/ilastik/ilastik/pull/2759
bump tiktorch by @k-dominik in https://github.com/ilastik/ilastik/pull/2765
exclude broken xarray version in conda pkg by @k-dominik in https://github.com/ilastik/ilastik/pull/2768

Full Changelog: https://github.com/ilastik/ilastik/compare/1.4.1b7...1.4.1b9

- Python
Published by k-dominik over 2 years ago

ilastik - 1.4.1b7

What's Changed

fix test mouse move by @k-dominik in https://github.com/ilastik/ilastik/pull/2736
make NN-related operators aware of tensor ids by @k-dominik in https://github.com/ilastik/ilastik/pull/2732
replace vigra for tiff reading with tifffile by @k-dominik in https://github.com/ilastik/ilastik/pull/2733
bigger shape in 'z' for tiffs means faster browsing by @k-dominik in https://github.com/ilastik/ilastik/pull/2737
Fix devenv by @k-dominik in https://github.com/ilastik/ilastik/pull/2726
Disabled addRemoveData test by @k-dominik in https://github.com/ilastik/ilastik/pull/2742
Undo elf fix by @k-dominik in https://github.com/ilastik/ilastik/pull/2734
Data input: Phrase axistags error message more user-friendly by @btbest in https://github.com/ilastik/ilastik/pull/2747
First try most compatible H5 saving, otherwise use v1.8 by @oanegros in https://github.com/ilastik/ilastik/pull/2746
reduce number of deprecation warnings by @k-dominik in https://github.com/ilastik/ilastik/pull/2740
Request object features per plugin in parallel by @k-dominik in https://github.com/ilastik/ilastik/pull/2750
experimental API refactor by @k-dominik in https://github.com/ilastik/ilastik/pull/2752

Experimental API changes

the generic ilastik.experimental.api.from_project_file function is now deprecated. Please use ilastik.experimental.api.PixelClassificationPipeline.from_ilp_file instead. New workflows will be made available only in the explicit fashion in the future. Also the PixelClassificationPipeline.predict method was deprecated in favor of a more explicit PixelClassificationPipeline.get_probabilities method. Idea is to add get_OUTPUT methods to existing/new piplelines that match the headless export names.

New Contributors

@oanegros made their first contribution in https://github.com/ilastik/ilastik/pull/2746

Full Changelog: https://github.com/ilastik/ilastik/compare/1.4.1b6...1.4.1b7

- Python
Published by k-dominik over 2 years ago

ilastik - 1.4.1b6

What's Changed

Restyle label table by @btbest in https://github.com/ilastik/ilastik/pull/2710
bump python version to 3.9 by @k-dominik in https://github.com/ilastik/ilastik/pull/2703
Support for Apple Silicon (Osx on arm 64) by @k-dominik in https://github.com/ilastik/ilastik/pull/2709
increase timeout to launch tiktorch by @k-dominik in https://github.com/ilastik/ilastik/pull/2720
Fix conservation tracking tests by @btbest in https://github.com/ilastik/ilastik/pull/2716
unfreeze cache before exporting data from tda workflow by @k-dominik in https://github.com/ilastik/ilastik/pull/2723
hacky fix for elf limiting threads by @k-dominik in https://github.com/ilastik/ilastik/pull/2724

Full Changelog: https://github.com/ilastik/ilastik/compare/1.4.1b1...1.4.1b6

- Python
Published by k-dominik over 2 years ago

ilastik - 1.4.1b1

What's Changed

fix elf ws now returns uint64 by @k-dominik in https://github.com/ilastik/ilastik/pull/2690
mnt: update pytorch versions by @k-dominik in https://github.com/ilastik/ilastik/pull/2692
mnt: wsdt package not used by @k-dominik in https://github.com/ilastik/ilastik/pull/2685
functionality to ignore multiple dirty propagations from same source by @k-dominik in https://github.com/ilastik/ilastik/pull/2694
- this enables faster stage 1 retraining in autocontext if stage 2 has already been trained
release pin on pytest by @k-dominik in https://github.com/ilastik/ilastik/pull/2633
Add Trainable Domain Adaptation workflow by @k-dominik in https://github.com/ilastik/ilastik/pull/2704
Rearrange labeling UI by @btbest in https://github.com/ilastik/ilastik/pull/2705
fix tda export names by @k-dominik in https://github.com/ilastik/ilastik/pull/2708

Full Changelog: https://github.com/ilastik/ilastik/compare/1.4.0...1.4.1b1

- Python
Published by k-dominik over 2 years ago

ilastik - 1.4.0

Highlights

Neural Network Workflow: run pre-trained neural networks from Bioimage.io Model Zoo in ilastik
- Networks can run on CPU, GPU (choose the GPU build for Windows, or Linux), or on a remote server
- No Neural Network training, yet - we’re working on it.
New startup screen!
- Major UI and performance improvements for the Multicut Workflow
- Stability/Usability improvements in the Carving Workflow
- By popular demand: redo/undo for brush-strokes
- Many bugfixes throughout

Downloads

Please visit our website for more information.

GPU-enabled builds (will make running the Neural Network Workflow faster if you have a compatible nvidia GPU in your machine): * Windows * Linux

ilastik can also be installed via conda/mamba, see our Readme.

- Python
Published by k-dominik about 3 years ago