Using pyLSM to read LSM files in Python

The good people at Janelia have provided the fly community with an enormous wealth of data in the form of confocal stacks of their GAL4 collection. There are many excellent open source tools to work with such image collections (e.g. imagej and fluorender), but reading the stacks directly into Python for automated analysis can be difficult. Below I'll describe my preferred method.

First, download the zipped PyLSM folder from here. (Linked to from this page.)

Next, unzip the folder, navigate inside it at a command prompt, and run

sudo python setup.py install

The website for this python module is http://www.freesbi.ch/en/pylsm and there is some documentation here.

I haven't tried out the gui yet, but here is a snippet of code that should open a Janelia stack.

	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.)

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