NanoImagingPack 2.1.5

An image processing package meant for use in the optics and microscopy community

NanoImagingPack

This is a package for simple image processing. It is oriented on the DIP-Image package, which is available for Matlab. The goal is to keep things simple and make it available for a broad community.

Installation

1. Download Anaconda https://docs.anaconda.com/anaconda/install/
2. Open an anaconda prompt
3. create a new environment (tested in Python 3.8)

   conda create --name nanoimaging python=3.8 anaconda tifffile
   

4. Activate

   conda activate nanoimaging
   

5. Install this feature branch of NanoImagingPack

   pip install git+https://gitlab.com/bionanoimaging/nanoimagingpack
   

Getting started

Start an ipython shell

ipython

Load and view a sample image

import NanoImagingPack as nip
import napari

img = nip.readim("erika")
nip.vv(img)

The created image is of type "image"

Gain calibration from an inhomogenous stack

Perform a gain calibration using simulated data.

import NanoImagingPack as nip
import numpy as np

# define the input parameters
NPHOT = 100 # max number of photons in simulation
OFFSET = 100 # black level offset
READNOISE = 4 # read noise to simulate
STACK_SIZE = 30

img = nip.readim("MITO_SIM")[0] # load the first frame from the MITO_SIM sample

fg = np.tile(img,(STACK_SIZE,1,1)) # make a stack of frames
fg = nip.poisson(fg, NPhot=NPHOT) # simulate poissonian shot noise

fg = fg + np.random.normal(loc=OFFSET, scale=READNOISE, size=fg.shape) # add gaussian noise

bg = np.random.normal(loc=OFFSET, scale=READNOISE, size=fg.shape) # generate background stack

# perform a calibration and plot the results
nip.cal_readnoise(fg, bg, brightness_blurring=False)

Notes

• the command nip.lookfor('some string') allows you to search for functions and methods
• nip.view() or nip.vv() provides an image viewer
  • The default viewer is currently Napari, but this can be changed by nip.setDefault('IMG_VIEWER',myViewer) with myViewer being one of 'NIP_VIEW', 'VIEW5D','NAPARI','INFO'
  • in NIP_VIEW press 'h' to get help. In VIEW5d press "?"
• graph() provides a simple viewer for 2D graphs -> you can add lists for multiple graphs

Features

• multidimensional fft/ifft
• image alignment
• finding for SLM based SIM images
• Controlling Hamamatsu LCOS SLM
• Creating OTFs, PSFs etc.
• Image manipulation (convolution, (simple) EdgeDamping, extracting, concattenating, Fourier-space extractions and padding)
• helper functions such as ramps, xx, yy, zz, freq/realspace coord transforms

See "dependencies.txt" for help required dependencies