From c102195b3d08033eaf932fa4f33f2b9faf3be3c8 Mon Sep 17 00:00:00 2001 From: Lorenzo Gaifas Date: Wed, 7 Aug 2024 16:03:14 +0200 Subject: [PATCH] update readme with sphere and TODO in docs (#180) --- README.md | 6 ++++-- docs/getting_started.md | 8 ++++++++ 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 9323acc..4cb2dcf 100644 --- a/README.md +++ b/README.md @@ -3,6 +3,7 @@ # blik [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10090438.svg)](https://zenodo.org/doi/10.5281/zenodo.10090438) +[![Paper DOI](https://zenodo.org/badge/DOI/10.1371/journal.pbio.3002447.svg)](https://doi.org/10.1371/journal.pbio.3002447) [![License](https://img.shields.io/pypi/l/blik.svg?color=green)](https://github.com/brisvag/blik/raw/main/LICENSE) [![PyPI](https://img.shields.io/pypi/v/blik.svg?color=green)](https://pypi.org/project/blik) [![Python Version](https://img.shields.io/pypi/pyversions/blik.svg?color=green)](https://python.org) @@ -54,13 +55,14 @@ The `-w blik` is important for proper initialization of all the layers. Always o The main widget has a few functions: - `experiment`: quickly switch to a different experiment id (typically, everything related to an individual tomogram such as volume, particles and segmentations) -- `new`: generate a new `segmentation`, a new manually-picked set of `particles`, or a new `surface picking` or `filament picking` for segmentation, particle generation or volume resampling. +- `new`: generate a new `segmentation`, a new manually-picked set of `particles`, or a new `surface`, `sphere`, or `filament picking` for segmentation, particle generation or volume resampling. - `add to exp`: add a layer to the currently selected `experiment` (just a shorthand for `layer.metadata['experiment_id'] = current_exp_id`) - `slice_thickness`: changes the slicing thickness in all dimensions in napari. Images will be averaged over that thickness, and all particles in the slice will be displayed. -There are also widgets for picking of both surfaces and filaments. +There are also widgets for picking surfaces, spheres and filaments: - `surface`: process a previously picked `surface picking` layer to generate a surface mesh and distribute particles on it for subtomogram averaging, or resample a tomogram along the surface. +- `sphere`: process a previously picked `sphere picking` layer to generate a sphere mesh and distribute particles on it for subtomogram averaging. - `filament`: process a previously picked `filament picking` layer to generate a filament and distribute particles on it for subtomogram averaging, or resample a tomogram along the filament. # References diff --git a/docs/getting_started.md b/docs/getting_started.md index 1f24cfd..2f5b68b 100644 --- a/docs/getting_started.md +++ b/docs/getting_started.md @@ -180,6 +180,14 @@ name: surface_particles Particles uniformly distributed on the generated surface. ``` +### Surface from a segmentation + +TODO! + +### Sphere picking + +TODO! + ### Filament picking Another geometrical picking model implemented in blik is the `filament picker`. The procedure is similar to that for surfaces. To start defining a new filament, we need to create a new `filament picking` in the main widget. This will open a new `Points` layer called `filament picks`.