{"name":"blik","display_name":"blik","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"blik.get_reader","title":"Open data with blik","python_name":"blik.reader:get_reader","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"blik.write_image","title":"Save image data with blik","python_name":"blik.writer:write_image","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"blik.write_labels","title":"Save labels data with blik","python_name":"blik.writer:write_image","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"blik.write_particles_relion_30","title":"Save particles data with blik (relion 3.0)","python_name":"blik.writer:write_particles_relion_30","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"blik.write_particles_relion_31","title":"Save particles data with blik (relion 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widget","python_name":"blik.widgets.power_spectrum:power_spectrum","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"blik.get_reader","filename_patterns":["*.mrc","*.mrcs","*.st","*.map","*.hdf","*.em","*.star","*.tbl","*.box","*.cbox","*.picks","*.surf"],"accepts_directories":false}],"writers":[{"command":"blik.write_image","layer_types":["image"],"filename_extensions":[".mrc",".mrcs",".st"],"display_name":"image"},{"command":"blik.write_labels","layer_types":["labels"],"filename_extensions":[".mrc",".mrcs",".st"],"display_name":"segmentation"},{"command":"blik.write_particles_relion_30","layer_types":["points+","vectors*"],"filename_extensions":[".star"],"display_name":"particles (relion 3.0)"},{"command":"blik.write_particles_relion_31","layer_types":["points+","vectors*"],"filename_extensions":[".star"],"display_name":"particles (relion 3.1)"},{"command":"blik.write_particles_relion_40","layer_types":["points+","vectors*"],"filename_extensions":[".star"],"display_name":"particles (relion 4.0)"},{"command":"blik.write_surface_picks","layer_types":["shapes"],"filename_extensions":[".picks"],"display_name":"surface picks"},{"command":"blik.write_surface","layer_types":["surface"],"filename_extensions":[".surf"],"display_name":"surface mesh"}],"widgets":[{"command":"blik.main_widget","display_name":"main widget","autogenerate":false},{"command":"blik.file_reader","display_name":"file reader","autogenerate":false},{"command":"blik.bandpass_filter","display_name":"bandpass filter","autogenerate":false},{"command":"blik.gaussian_filter","display_name":"gaussian filter","autogenerate":false},{"command":"blik.power_spectrum","display_name":"power spectrum","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"blik","version":"0.5.5","dynamic":null,"platform":null,"supported_platform":null,"summary":"Python tool for visualising and interacting with cryo-ET and subtomogram averaging data.","description":"![logo](https://github.com/brisvag/blik/raw/main/docs/images/logo.png)\n\n# blik\n\n[![License](https://img.shields.io/pypi/l/blik.svg?color=green)](https://github.com/brisvag/blik/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/blik.svg?color=green)](https://pypi.org/project/blik)\n[![Python Version](https://img.shields.io/pypi/pyversions/blik.svg?color=green)](https://python.org)\n[![CI](https://github.com/brisvag/blik/actions/workflows/ci.yml/badge.svg)](https://github.com/brisvag/blik/actions/workflows/ci.yml)\n[![codecov](https://codecov.io/gh/brisvag/blik/branch/main/graph/badge.svg)](https://codecov.io/gh/brisvag/blik)\n\n![blik showcase](https://user-images.githubusercontent.com/23482191/161224963-ad746a06-c2e5-46fe-a13b-f356bc4ad72b.png)\n\n**`blik`** is a tool for visualising and interacting with cryo-ET and subtomogram averaging data. It leverages the fast, multi-dimensional [napari viewer](https://napari.org) and the scientific python stack.\n\n**DISCLAIMER**: this package is in development phase. Expect bugs and crashes. Please, report them on the issue tracker and ask if anything is unclear!\n\n## Installation\n\nYou can either install `blik` through the [napari plugin system](https://napari.org/plugins/index.html), through pip, or get both napari and blik directly with:\n\n```bash\npip install \"blik[all]\"\n```\n\nThe `[all]` qualifier also installs `pyqt5` as the napari GUI backend, and a few additional napari plugins that you might find useful in your workflow:\n- [napari-properties-plotter](https://github.com/brisvag/napari-properties-plotter)\n- [napari-properties-viewer](https://github.com/kevinyamauchi/napari-properties-viewer)\n- [napari-label-interpolator](https://github.com/kevinyamauchi/napari-label-interpolator)\n\n## Basic Usage\n\nFrom the command line:\n```bash\nnapari -w blik -- /path/to.star /path/to/mrc/files/*\n```\n\nThe `-w blik` is important for proper initialization of all the layers. Keep the main widget open to ensure nothing goes wrong!\n\n*`blik` is just `napari`*. Particles and images are exposed as simple napari layers, which can be analysed and manipulated with simple python, and most importantly other [napari plugins](https://napari-hub.org/).\n\n## Widget\n\nThe main widget has a few functions:\n\n- `experiment`: quickly switch to a different experiment id (typically, everything related to an individual tomogram such as volume, particles and segmentations)\n- `new`: generate a new `segmentation`, a new manually-picked set of `particles`, or a new `surface picking` for segmentation or particle generation\n- `add to exp`: add a layer to the currently selected `experiment` (just a shorthand for `layer.metadata['experiment_id'] = current_exp_id`)\n- `surface`: process a previously picked `surface picking` layer to generate a surface mesh or distribute particles on it for subtomogram averaging.\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":null,"author_email":"Lorenzo Gaifas <brisvag@gmail.com>","maintainer":null,"maintainer_email":null,"license":"GPLv3","classifier":["Development Status :: 3 - Alpha","Framework :: napari","License :: OSI Approved :: GNU General Public License v3 (GPLv3)","Natural Language :: English","Programming Language :: Python :: 3","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Programming Language :: Python :: 3.11","Topic :: Scientific/Engineering :: Visualization","Typing :: Typed"],"requires_dist":["cryohub>=0.5.1","cryotypes>=0.2.0","dask","einops","magicgui>=0.4.0","morphosamplers>=0.0.5","numpy","pandas","scipy","napari-label-interpolator; extra == 'all'","napari-properties-plotter; extra == 'all'","napari-properties-viewer; extra == 'all'","napari[all]>=0.4.18; extra == 'all'","black; extra == 'dev'","blik[test]; extra == 'dev'","ipython; extra == 'dev'","mypy; extra == 'dev'","pdbpp; extra == 'dev'","pre-commit; extra == 'dev'","rich; extra == 'dev'","ruff; extra == 'dev'","napari[all]>=0.4.18; extra == 'test'","pytest-cov; extra == 'test'","pytest-qt; extra == 'test'","pytest>=6.0; extra == 'test'"],"requires_python":">=3.9","requires_external":null,"project_url":["homepage, https://github.com/brisvag/blik","repository, https://github.com/brisvag/blik"],"provides_extra":["all","dev","test"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}