From 5d56242b98d6019a367bf66e1c8bc41649d9cff2 Mon Sep 17 00:00:00 2001 From: brisvag Date: Thu, 30 Nov 2023 11:22:16 +0000 Subject: [PATCH] deploy: 7c69ed3d81a50fd667df3fd5ef4db74be0cf2398 --- index.html | 2 +- searchindex.js | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/index.html b/index.html index 6a638b8..7e5c8a0 100644 --- a/index.html +++ b/index.html @@ -2,4 +2,4 @@

The [all] qualifier also installs pyqt5 as the napari GUI backend, and a few additional napari plugins that you might find useful in your workflow:

Nightly build

If you’d like the most up to date blik possible, you can install directly from the main branch on github. This also uses napari main, so expect some instability!

pip install "git+https://github.com/brisvag/blik.git@main#egg=blik[all]"
 pip install "git+https://github.com/napari/napari.git@main#egg=napari[all]"

Basic Usage

From the command line:

napari -w blik -- /path/to.star /path/to/mrc/files/*
-

The -w blik is important for proper initialization of all the layers. Always open the main widget open to ensure nothing goes wrong!

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.

Widgets

The main widget has a few functions:

There are also widgets for picking of both surfaces and filaments.

\ No newline at end of file +

The -w blik is important for proper initialization of all the layers. Always open the main widget open to ensure nothing goes wrong!

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.

Widgets

The main widget has a few functions:

There are also widgets for picking of both surfaces and filaments.

\ No newline at end of file diff --git a/searchindex.js b/searchindex.js index a4f7b64..2d47ff3 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["getting_started", "index"], "filenames": ["getting_started.md", "index.md"], "titles": ["Getting started", "blik"], "terms": {"from": [0, 1], "command": [0, 1], "line": [0, 1], "napari": [0, 1], "w": [0, 1], "blik": 0, "path": [0, 1], "star": [0, 1], "mrc": [0, 1], "The": [0, 1], "import": [0, 1], "proper": [0, 1], "initi": [0, 1], "all": [0, 1], "layer": [0, 1], "keep": 0, "open": [0, 1], "ensur": [0, 1], "noth": [0, 1], "goe": [0, 1], "wrong": [0, 1], "In": 0, "gui": [0, 1], "you": [0, 1], "ll": 0, "find": [0, 1], "select": [0, 1], "which": [0, 1], "experi": [0, 1], "id": [0, 1], "visual": 0, "dropdown": 0, "menu": 0, "relev": 0, "made": 0, "visibl": 0, "here": 0, "can": [0, 1], "also": [0, 1], "creat": 0, "new": [0, 1], "segment": [0, 1], "simpl": [0, 1], "label": [0, 1], "automat": 0, "add": [0, 1], "current": [0, 1], "thi": [0, 1], "save": 0, "have": 0, "correct": 0, "metadata": [0, 1], "ani": 0, "exist": 0, "us": [0, 1], "If": [0, 1], "need": 0, "finer": 0, "control": 0, "over": 0, "allow": 0, "addit": [0, 1], "argument": 0, "compar": 0, "basic": 0, "interfac": 0, "name_regex": 0, "regex": 0, "pattern": 0, "extract": 0, "tomogram": [0, 1], "name": 0, "thing": 0, "like": [0, 1], "rlnmicrographnam": 0, "By": 0, "default": 0, "recogn": 0, "contain": 0, "ts_": 0, "d": [0, 1], "fall": 0, "back": 0, "For": 0, "exampl": 0, "follow": 0, "assign": 0, "ts_001": 0, "coolsample2_ts_001_someth": 0, "particles_ts_001": 0, "These": 0, "instead": 0, "just": [0, 1], "02": 0, "image_02": 0, "em": 0, "particles_02": 0, "tbl": 0, "whitelist": 0, "specif": 0, "pass": 0, "anyth": [0, 1], "list": 0, "won": 0, "t": 0, "imag": [0, 1], "gaussian": 0, "help": 0, "futur": 0, "avail": 0, "much": 0, "faster": 0, "gpu": 0, "base": 0, "interpol": [0, 1], "tool": 1, "visualis": 1, "interact": 1, "cryo": 1, "et": 1, "subtomogram": 1, "averag": 1, "data": 1, "It": 1, "leverag": 1, "fast": 1, "multi": 1, "dimension": 1, "viewer": 1, "scientif": 1, "python": 1, "stack": 1, "disclaim": 1, "packag": 1, "develop": 1, "phase": 1, "expect": 1, "bug": 1, "crash": 1, "pleas": 1, "report": 1, "them": 1, "issu": 1, "tracker": 1, "ask": 1, "unclear": 1, "either": 1, "through": 1, "plugin": 1, "system": 1, "pip": 1, "get": 1, "both": 1, "directli": 1, "qualifi": 1, "pyqt5": 1, "backend": 1, "few": 1, "might": 1, "your": 1, "workflow": 1, "properti": 1, "plotter": 1, "most": 1, "up": 1, "date": 1, "possibl": 1, "main": 1, "branch": 1, "github": 1, "so": 1, "some": 1, "instabl": 1, "git": 1, "http": 1, "com": 1, "brisvag": 1, "egg": 1, "file": 1, "alwai": 1, "particl": 1, "ar": 1, "expos": 1, "analys": 1, "manipul": 1, "importantli": 1, "other": 1, "ha": 1, "function": 1, "quickli": 1, "switch": 1, "differ": 1, "typic": 1, "everyth": 1, "relat": 1, "an": 1, "individu": 1, "volum": 1, "gener": 1, "manual": 1, "pick": 1, "set": 1, "surfac": 1, "filament": 1, "resampl": 1, "exp": 1, "shorthand": 1, "experiment_id": 1, "current_exp_id": 1, "There": 1, "process": 1, "previous": 1, "mesh": 1, "distribut": 1, "along": 1}, "objects": {}, "objtypes": {}, "objnames": {}, "titleterms": {"get": 0, "start": 0, "load": 0, "data": 0, "widget": [0, 1], "main": 0, "file": 0, "reader": 0, "filter": 0, "blik": 1, "instal": 1, "nightli": 1, "build": 1, "basic": 1, "usag": 1}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 6, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1, "sphinx": 56}}) \ No newline at end of file +Search.setIndex({"docnames": ["getting_started", "index"], "filenames": ["getting_started.md", "index.md"], "titles": ["Getting started", "blik"], "terms": {"from": [0, 1], "command": [0, 1], "line": [0, 1], "napari": [0, 1], "w": [0, 1], "blik": 0, "path": [0, 1], "star": [0, 1], "mrc": [0, 1], "The": [0, 1], "import": [0, 1], "proper": [0, 1], "initi": [0, 1], "all": [0, 1], "layer": [0, 1], "keep": 0, "open": [0, 1], "ensur": [0, 1], "noth": [0, 1], "goe": [0, 1], "wrong": [0, 1], "In": 0, "gui": [0, 1], "you": [0, 1], "ll": 0, "find": [0, 1], "select": [0, 1], "which": [0, 1], "experi": [0, 1], "id": [0, 1], "visual": 0, "dropdown": 0, "menu": 0, "relev": 0, "made": 0, "visibl": 0, "here": 0, "can": [0, 1], "also": [0, 1], "creat": 0, "new": [0, 1], "segment": [0, 1], "simpl": [0, 1], "label": [0, 1], "automat": 0, "add": [0, 1], "current": [0, 1], "thi": [0, 1], "save": 0, "have": 0, "correct": 0, "metadata": [0, 1], "ani": 0, "exist": 0, "us": [0, 1], "If": [0, 1], "need": 0, "finer": 0, "control": 0, "over": [0, 1], "allow": 0, "addit": [0, 1], "argument": 0, "compar": 0, "basic": 0, "interfac": 0, "name_regex": 0, "regex": 0, "pattern": 0, "extract": 0, "tomogram": [0, 1], "name": 0, "thing": 0, "like": [0, 1], "rlnmicrographnam": 0, "By": 0, "default": 0, "recogn": 0, "contain": 0, "ts_": 0, "d": [0, 1], "fall": 0, "back": 0, "For": 0, "exampl": 0, "follow": 0, "assign": 0, "ts_001": 0, "coolsample2_ts_001_someth": 0, "particles_ts_001": 0, "These": 0, "instead": 0, "just": [0, 1], "02": 0, "image_02": 0, "em": 0, "particles_02": 0, "tbl": 0, "whitelist": 0, "specif": 0, "pass": 0, "anyth": [0, 1], "list": 0, "won": 0, "t": 0, "imag": [0, 1], "gaussian": 0, "help": 0, "futur": 0, "avail": 0, "much": 0, "faster": 0, "gpu": 0, "base": 0, "interpol": [0, 1], "tool": 1, "visualis": 1, "interact": 1, "cryo": 1, "et": 1, "subtomogram": 1, "averag": 1, "data": 1, "It": 1, "leverag": 1, "fast": 1, "multi": 1, "dimension": 1, "viewer": 1, "scientif": 1, "python": 1, "stack": 1, "disclaim": 1, "packag": 1, "develop": 1, "phase": 1, "expect": 1, "bug": 1, "crash": 1, "pleas": 1, "report": 1, "them": 1, "issu": 1, "tracker": 1, "ask": 1, "unclear": 1, "either": 1, "through": 1, "plugin": 1, "system": 1, "pip": 1, "get": 1, "both": 1, "directli": 1, "qualifi": 1, "pyqt5": 1, "backend": 1, "few": 1, "might": 1, "your": 1, "workflow": 1, "properti": 1, "plotter": 1, "most": 1, "up": 1, "date": 1, "possibl": 1, "main": 1, "branch": 1, "github": 1, "so": 1, "some": 1, "instabl": 1, "git": 1, "http": 1, "com": 1, "brisvag": 1, "egg": 1, "file": 1, "alwai": 1, "particl": 1, "ar": 1, "expos": 1, "analys": 1, "manipul": 1, "importantli": 1, "other": 1, "ha": 1, "function": 1, "quickli": 1, "switch": 1, "differ": 1, "typic": 1, "everyth": 1, "relat": 1, "an": 1, "individu": 1, "volum": 1, "gener": 1, "manual": 1, "pick": 1, "set": 1, "surfac": 1, "filament": 1, "resampl": 1, "exp": 1, "shorthand": 1, "experiment_id": 1, "current_exp_id": 1, "slice_thick": 1, "chang": 1, "slice": 1, "thick": 1, "dimens": 1, "displai": 1, "There": 1, "process": 1, "previous": 1, "mesh": 1, "distribut": 1, "along": 1}, "objects": {}, "objtypes": {}, "objnames": {}, "titleterms": {"get": 0, "start": 0, "load": 0, "data": 0, "widget": [0, 1], "main": 0, "file": 0, "reader": 0, "filter": 0, "blik": 1, "instal": 1, "nightli": 1, "build": 1, "basic": 1, "usag": 1}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 6, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1, "sphinx": 56}}) \ No newline at end of file