{"name":"psf-analysis-CFIM","display_name":"psf-analysis-CFIM","visibility":"public","icon":"","categories":[],"schema_version":"0.1.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"psf-analysis-CFIM.PsfAnalysis","title":"Create Psf Analysis","python_name":"psf_analysis_CFIM._dock_widget:PsfAnalysis","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"psf-analysis-CFIM.czi_reader.read_czi","title":"Read CZI File","python_name":"psf_analysis_CFIM.czi_reader.czi_reader_CFIM:read_czi","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"psf-analysis-CFIM.czi_reader.read_czi","filename_patterns":["*.czi"],"accepts_directories":false}],"writers":null,"widgets":[{"command":"psf-analysis-CFIM.PsfAnalysis","display_name":"PSF Analysis - CFIM","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"psf-analysis-CFIM","version":"1.7.10","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"A continuation of napari_psf_analysis, developed for CFIM - KU","description":"# psf-analysis-CFIM\n\n[![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/psf-analysis-CFIM)](https://napari-hub.org/plugins/psf-analysis-CFIM)\n\n---\n![application_screenshot](figs/PSF_CFIM_demo_v170.gif)\n\n## Installation\n\nYou can install this package using one of the following options:\n```bash\n  pip install psf-analysis-CFIM -U\n```\nFor the latest stable version (recommended)\n\n---\n\nor\n\n```bash\n  pip install git+https://github.com/MaxusTheOne/napari-psf-analysis-CFIM-edition\n```\nTo install the latest version (not guaranteed to be stable)\n\n---\nAdditionally, it can be installed via napari plugin manager under the name **psf-analysis-CFIM**.\n\n## About\n\nThis is a **fork** of the [napari-psf-analysis](https://github.com/fmi-faim/napari-psf-analysis) project.\n\nThe features from this edition are made as requested by the staff at CFIM.\n\nPlease contact me through Github or mail for any issues or help with development\n---\n\n## Extra Features\n\nThis edition includes the following additional features:\n\n- **Bulk Analysis for channels**: Allows for bulk analysis of multiple channels.\n  - **Combined Summary**: Adds a combined summary of all channels.\n  - **Channel Offset Table**: Adds a table with the relative offset of the channels.\n- **Bead Averaging**: Adds an image of an averaged bead from all selected.\n- **Visualisation**: Improves visualisation of the psf. Most notable color by wavelength.\n  - **Range indicator** Button to mark the min and max values of the image.\n- **PSF Report**: Adds a graded report on the quality of the PSF. <- WIP\n- **Bead Detection**: Detects beads in the image.\n- **Auto-Filling of Plugin Parameters**: Automatically populates parameters for the plugin.\n  - At least 1 input also looks better\n- **Auto Analysis of Image for PSF**: Performs automatic image analysis to ascertain the quality.\n- **CZI Reader**: Adds support for reading CZI image files.\n- **Debugging**: Adds a debug class to the IPython console. Small, but hey, we can show the psf box\n- **Error Handling**: Less likely to crash. errors points can be seen in viewer | Error UI.\n- **Bug fixes**: Fixes bugs involving zyx boxes, loading bar and other issues.\n\n## Known Issues\n\n- for autofilling, only .czi files are supported. Unlikely to work with other formats.\n- Installing plugin under paths including non-ASCII characters, like \"æøå\" cause unintended behavior.\n- The output.csv file is comma seperated with dot as decimal seperator, this might require a legacy workaround in programs like Excel.\n- Intensity for bead finder is hardcoded for now.\n- Some images might still crash in the analysis.\n- Might have missed some requirements\n\n\n## License\n\nDistributed under the terms of the [BSD-3] license,\n\"psf-analysis-CFIM\" is free and open source software\n","description_content_type":"text/markdown","keywords":null,"home_page":"https://github.com/MaxusTheOne/napari-psf-analysis-CFIM-edition","download_url":null,"author":"Markus L. Bille","author_email":"github+Markus@bille.dk","maintainer":null,"maintainer_email":null,"license":"BSD-3-Clause","classifier":["Development Status :: 5 - Production/Stable","Framework :: napari","Intended Audience :: Science/Research","License :: OSI Approved :: BSD License","Operating System :: OS Independent","Programming Language :: Python","Topic :: Scientific/Engineering :: Image Processing","Topic :: Scientific/Engineering :: Bio-Informatics","Topic :: Scientific/Engineering :: Visualization"],"requires_dist":["aicsimageio","aicspylibczi","matplotlib<3.9","matplotlib-inline","matplotlib-scalebar","napari[all]","numpy<2.0,>=1.26","pandas","pydantic","PyYAML","QtPy","scipy","reportlab","napari; extra == \"testing\"","pyqt5; extra == \"testing\"","tox; extra == \"testing\""],"requires_python":">=3.9","requires_external":null,"project_url":["Documentation, https://github.com/MaxusTheOne/napari-psf-analysis-CFIM-edition#README.md","Source Code, https://github.com/MaxusTheOne/napari-psf-analysis-CFIM-edition","Issue Tracker, https://github.com/MaxusTheOne/napari-psf-analysis-CFIM-edition/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}