napari-particles (WIP)

A particle layer for napari (super rough draft)

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Extension of Napari Particles that provides a dock widget within Napari into which .hdf5 (Picasso), .smlm, .csv (Thunderstorm) and .h5 files can be imported and rendered via drag and drop.

Installation

For the time being, the easiest way to install is as follows:

create an enviroment, e.g. using anaconda terminal with

conda create --name napari-particles
activate napari-particles

clone this repository using and install it using

git clone https://github.com/LREIN663/napari-particles
cd napari-particles
pip install -r requirements.txt

Usage

active the created enviroment in the anaconda terminal and start napari

activate napari-particles
napari

Now under plugins click napari-particles: SMLMQW and the dock widget should open. Now you can either use the import button or simply drag the file you are trying to open onto the list.

Usage (Original Repo)

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