Open a LSM image stack and display a maximum Z projection

open_lsm.py

import numpy as np
import matplotlib.pyplot as plt
plt.ion()
from pylsm import lsmreader

imageFile = lsmreader.Lsmimage(lsmFileName)
imageFile.open()

xLen = imageFile.header['Image'][0]['CZ LSM info']['Dimension X']
yLen = imageFile.header['Image'][0]['CZ LSM info']['Dimension Y']
zLen = imageFile.header['Image'][0]['CZ LSM info']['Dimension Z']
numColors = 3

frames = np.zeros((xLen, yLen, zLen, numColors),dtype='uint16')

for zPos in range(zLen):

    redData = np.flipud(imageFile.get_image(stack=zPos, channel=1))
    grnData = np.flipud(imageFile.get_image(stack=zPos, channel=0))
    frames[:,:,zPos,0] = redData
    frames[:,:,zPos,1] = grnData

fig = plt.figure()
ax = fig.add_subplot(111)
ax.imshow(frames.max(2)/4096.)