nvladimus

# Export your favorite Matplotlib colormap to Imaris look-up table (.pal file)
# Authors: ChatGPT and Nikita Vladimirov
# License: GPL3
import matplotlib.cm as cm
cmap = cm.get_cmap('plasma')
output_file = './plasma_palette_8bit.pal'
with open(output_file, 'w') as f:
    # Write the RGB values of each color in the colormap as text strings
    for i in range(256):
        rgba = cmap(i)

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nvladimus

# Compute FWHM(x,y) using 2D Gaussian fit, min-square optimization
# Optimization fits 2D gaussian: center, sigmas, baseline and amplitude
# works best if there is only one blob and it is close to the image center.
# author: Nikita Vladimirov @nvladimus (2018).
# based on code example: https://stackoverflow.com/questions/21566379/fitting-a-2d-gaussian-function-using-scipy-optimize-curve-fit-valueerror-and-m

import numpy as np
import scipy.optimize as opt

def twoD_GaussianScaledAmp((x, y), xo, yo, sigma_x, sigma_y, amplitude, offset):

nvladimus

# This python code uses MicroManager device drivers to control a camera. 
# Tested on Hamamatsu Orca Flash 4 camera, should work similarly on other cameras.
# Original idea: Kay Schink @koschink
# Gist implementation: Nikita Vladimirov @nvladimus

#Environment setup instructions: https://micro-manager.org/wiki/Using_the_Micro-Manager_python_library
import sys
sys.path.append("C:\\Program Files\\Micro-Manager-1.4")
import MMCorePy #load MicroManager for device control
import matplotlib.pyplot as plt

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# Simple digital pulse generation with PyDAQmx library and NI DAQmx board
# Requires NI DAQmx drivers, Python 2.7 installed, Windows.
# Tested on NI PCIe-6321 board
# Gist author: Nikita Vladimirov @nvladimus
import PyDAQmx as pd
ctr_ini_delay = 0 # sec
ctr_period = 0.1 # sec
ctr_duty_cycle = 0.01
task = pd.Task()
task.CreateCOPulseChanFreq("Dev1/ctr0",  "CamTrigger",  pd.DAQmx_Val_Hz,  pd.DAQmx_Val_Low,   ctr_ini_delay,  1/float(ctr_period),  ctr_duty_cycle)