maweigert / napari-particles

napari-particles (WIP)

A particle layer for napari

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Installation

Clone the repo and install

git clone [e-mail]:maweigert/napari-particles.git
pip install napari-particles/

Usage

import numpy as np
import napari
from napari_particles.particles import Particles
from napari_particles.filters import ShaderFilter

coords = np.random.uniform(0,100,(10000,3))
coords[:,0] *=.1
size   = np.random.uniform(.4, 1, len(coords))
values = np.random.uniform(0.2,1, len(coords))

layer = Particles(coords,
                size=size,
                values=values,
                colormap='Spectral',
                filter = ShaderFilter('gaussian'))

layer.contrast_limits=(0,1)
v = napari.Viewer()
layer.add_to_viewer(v)
v.dims.ndisplay=3
v.camera.perspective=80.0
napari.run()

Examples Scripts

in ./examples

Basic

python test_particles.py

SMLM

If you have a localization csv file in the following format (with "\t" as separator)

"frame" "x [nm]"        "y [nm]"        "z [nm]"        "uncertainty_xy [nm]"   "uncertainty_z [nm]"
2       23556.7 2045    -97     2.5     5
2       5871.4  2853.1  -306    2.2     4.5
2       24767.5 3298    -267    1.7     3.5
2       22070.8 3502.8  -334    1       2
....

you can render it like so:

python test_smlm.py -i data.csv