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This repository was archived by the owner on Mar 26, 2026. It is now read-only.
Could you kindly explain the difference between get_frame() and get_plane()? And moving forward, which one are you going to keep?
I'm asking because on one of my confocal stacks, lif_image.get_frame(z=60, c=1) returns the right plane and channel image, whereas lif_image.get_plane(requested_dims={3:70}, c=1) returns an image for channel 0, no matter which value I pass to c in get_plane()
My image shows this metadata in FIJI:
Name
value
BitsPerPixel
16
DimensionOrder
XYCZT
IsInterleaved
false
IsRGB
false
LittleEndian
true
PixelType
uint16
Series 0 Name
ctrl 1
SizeC
2
SizeT
1
SizeX
2048
SizeY
2048
SizeZ
140
So, I came-up with my own as_array() which I saw is very similar to the one @haesleinhuepf wrote in #42
def as_array(lif_image, t=0, c=0, m=0):
"""Returns a LifImage as a numpy array for a given time-point, channel and mosaic image."""
frames = [lif_image.get_frame(z,t,c,m) for z in range(lif_image.dims.z)]
return np.asarray(frames)