From fae9c8ac5aa887483efc0fbf41688370f71d973f Mon Sep 17 00:00:00 2001 From: brisvag Date: Tue, 29 Aug 2023 11:50:36 +0000 Subject: [PATCH] deploy: 232825180a51ba71eb76605913108db4e955979b --- _static/pygments.css | 2 +- genindex.html | 2 +- getting_started.html | 4 ++-- index.html | 4 ++-- search.html | 2 +- 5 files changed, 7 insertions(+), 7 deletions(-) diff --git a/_static/pygments.css b/_static/pygments.css index 8f547f03..05f99f9f 100644 --- a/_static/pygments.css +++ b/_static/pygments.css @@ -1 +1 @@ -@charset "utf-8";pre{line-height:125%}td.linenos .normal{color:inherit;background-color:transparent;padding-left:5px;padding-right:5px}span.linenos{color:inherit;background-color:transparent;padding-left:5px;padding-right:5px}td.linenos .special{color:#000;background-color:#ffffc0;padding-left:5px;padding-right:5px}span.linenos.special{color:#000;background-color:#ffffc0;padding-left:5px;padding-right:5px}.highlight 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.sr{color:#A45A77}.highlight .s1{color:#BA2121}.highlight .ss{color:#19177C}.highlight .bp{color:#008000}.highlight .fm{color:#00F}.highlight .vc{color:#19177C}.highlight .vg{color:#19177C}.highlight .vi{color:#19177C}.highlight .vm{color:#19177C}.highlight .il{color:#666} \ No newline at end of file diff --git a/genindex.html b/genindex.html index fef399df..e76078db 100644 --- a/genindex.html +++ b/genindex.html @@ -1 +1 @@ - Index — Blik Skip to content

Index

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Index

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Getting started

Loading data

From the command line:

napari -w blik -- /path/to.star /path/to/mrc/files/*
+                        Getting started — Blik                                      Skip to content  
  
 
 
 
 
 
 
  
 
 
 
 
 
  
 
 
 
 
 
 
Getting started
 
 
Loading data
 
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. Keep the main widget open to ensure nothing goes wrong!
 
 
 
Widgets
 
 
Main Widget
 
In the napari GUI, you’ll find the main blik widget. Select which experiment ID to visualize with the dropdown menu, and the relevant layers will be selected and made visible.
 
Here you can also create a new segmentation (a simple napari labels layer) and automatically add it to the current experiment. This ensures that saving it will have all the correct metadata.
 
You can add any existing layer to the currently selected experiment ID by using the add layer widget.
 
 
 
File Reader
 
If you need finer control over loading data, you can use the file reader widget. You can also start it from the command line with:
 
napari -w blik 'file reader'
 
 
 
This widget allows additional arguments compared to the basic napari command line interface.
 
 
name_regex is a regex pattern used to extract tomogram names from file names (or things like the rlnMicrographName filed in .star files). By default, blik recognizes files containing TS_\d+, and will fall back to \d+. For example, the following files will be assigned TS_001:
 
CoolSample2_TS_001_something.mrc
 Particles_TS_001.star
 
 
 
These, instead, will be assigned just 02:
 
image_02.em
 particles_02.tbl
-
 
 
 
names can be used to whitelist specific tomogram names to load. If passed, anything not in the list won’t be loaded.
 
 
 
Filters
 
Simple imaging filters (such as gaussian) to help with visualization. In the future, these will be available as much faster gpu-based interpolations.
 
 
 
   
 
 
 
 
   
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names can be used to whitelist specific tomogram names to load. If passed, anything not in the list won’t be loaded.

Filters

Simple imaging filters (such as gaussian) to help with visualization. In the future, these will be available as much faster gpu-based interpolations.

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logo

blik

Codecov branch PyPI PyPI - Python Version

it means glance in Dutch

blik showcase

blik is a tool for visualising and interacting with cryo-ET and subtomogram averaging data. It leverages the fast, multi-dimensional napari viewer and the scientific python stack.

DISCLAIMER: this package is in development phase. Expect frequent bugs and crashes. Please, report them on the issue tracker and ask if anything is unclear!

Installation

You can either install blik through the napari plugin system, through pip, or get both napari and blik directly with:

pip install "blik[all]"
+                        blik — Blik                                      Skip to content  
  
 
 
 
 
 
 
  
 
 
 
 
 
  
 
 
 
 
 
logo
 
 
blik
 
Codecov branch PyPI PyPI - Python Version
 
it means glance in Dutch
 
blik showcase
 
blik is a tool for visualising and interacting with cryo-ET and subtomogram averaging data. It leverages the fast, multi-dimensional napari viewer and the scientific python stack.
 
DISCLAIMER: this package is in development phase. Expect frequent bugs and crashes. Please, report them on the issue tracker and ask if anything is unclear!
 
 
Installation
 
You can either install blik through the napari plugin system, through pip, or get both napari and blik directly with:
 
pip install "blik[all]"
 
 
 
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:
  
 
 
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. Keep 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.
 
 
 
Widget
 
The main widget has a few functions:
 
 
 
 
   
 
 
 
 
   
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+

The -w blik is important for proper initialization of all the layers. Keep 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.

Widget

The main widget has a few functions:

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Search

Please activate JavaScript to enable the search functionality.

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Search

Please activate JavaScript to enable the search functionality.

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