Voxel size of output-layer is different from input layer #37
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Hi @romainGuiet, thanks for reporting this issue. It turns out that it was presumably fixed in napari-apoc version 0.8.2. Can you check which version is installed on your computer? I also just tested it by annotating blobs.tif where voxel-size was 0.5 in X/Y and it worked. Could provide a minimum working example for reproducing the issue? Thanks! Best, |
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Hi @haesleinhuepf , I installed devbio-napari (last week) following the installation procedure described here I just ran a conda list and got for napari-accelerated-pixel-and-object-classification 0.12.3 pyhd8ed1ab_0 conda-forge (whole conda list result at the end of this message ) for a minimal example, dataset is on zenodo and I used the lines below in a notebook : from tifffile import imread # https://pypi.org/project/tifffile/#examples
import napari
import numpy as np
viewer = napari.Viewer()
viewer.show()
#we define the path
image_path = '../data/moss/Moss_Fused_Downsampled_Anisotropy_2.tif'
image = imread(image_path)
print ("image shape : " + str(image.shape))
# we set the voxel scale
scale = [2,1,1]
blending = 'additive'
# extract the green channel
green_ch = image[:,0,:,:]
viewer.add_image( green_ch ,
name="Green",
colormap='green' ,
scale=scale ,
blending=blending,
contrast_limits=[200,750]
)
magenta_ch = image[:,1,:,:]
viewer.add_image(magenta_ch,
name="Magenta",
colormap='magenta',
scale=scale ,
blending=blending,
contrast_limits=[300,3000]
)the manually use apoc and here is the results in 3D :
Cheers, R Here is the whole 'conda list' result : |
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I just noticed that you are using 0.5 in x and y. I tested to load using
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reported here: https://forum.image.sc/t/napari-accelerated-pixel-object-classification-apoc-output-scale-input-loading/77106
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