napari-accelerated-pixel-and-object-classification
napari-accelerated-pixel-and-object-classification copied to clipboard
Published
20 hours ago •
haesleinhuepf
haesleinhuepf
Voxel size of output-layer is different from input layer
reported here: https://forum.image.sc/t/napari-accelerated-pixel-object-classification-apoc-output-scale-input-loading/77106
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, Robert
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 :
>conda list
# packages in environment at C:\ProgramData\Anaconda3\envs\devbio:
#
# Name Version Build Channel
alabaster 0.7.13 pyhd8ed1ab_0 conda-forge
anyio 3.6.2 pyhd8ed1ab_0 conda-forge
aom 3.5.0 h63175ca_0 conda-forge
apoc-backend 0.12.0 pyhd8ed1ab_0 conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py39ha55989b_3 conda-forge
asciitree 0.3.3 py_2 conda-forge
asttokens 2.2.1 pyhd8ed1ab_0 conda-forge
attrs 22.2.0 pyh71513ae_0 conda-forge
autopep8 2.0.1 pyhd8ed1ab_0 conda-forge
babel 2.11.0 pyhd8ed1ab_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 pyhd8ed1ab_3 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.11.1 pyha770c72_0 conda-forge
bleach 6.0.0 pyhd8ed1ab_0 conda-forge
blosc 1.21.3 hdccc3a2_0 conda-forge
bokeh 2.4.3 pyhd8ed1ab_3 conda-forge
brotli 1.0.9 hcfcfb64_8 conda-forge
brotli-bin 1.0.9 hcfcfb64_8 conda-forge
brotlipy 0.7.0 py39ha55989b_1005 conda-forge
bzip2 1.0.8 h8ffe710_4 conda-forge
c-blosc2 2.6.1 h183a6f4_0 conda-forge
ca-certificates 2022.12.7 h5b45459_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachey 0.2.1 pyh9f0ad1d_0 conda-forge
certifi 2022.12.7 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py39h68f70e3_3 conda-forge
cfitsio 4.2.0 h9ebe7e4_0 conda-forge
charls 2.3.4 h39d44d4_0 conda-forge
charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge
click 8.1.3 win_pyhd8ed1ab_2 conda-forge
click-default-group 1.2.2 pyhd8ed1ab_1 conda-forge
cloudpickle 2.2.1 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comm 0.1.2 pyhd8ed1ab_0 conda-forge
conda 22.11.1 py39hcbf5309_1 conda-forge
conda-package-handling 2.0.2 pyh38be061_0 conda-forge
conda-package-streaming 0.7.0 pyhd8ed1ab_1 conda-forge
contourpy 1.0.7 py39h1f6ef14_0 conda-forge
cryptography 39.0.0 py39h58e9bdb_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cytoolz 0.12.0 py39ha55989b_1 conda-forge
czifile 2019.7.2 pyh9f0ad1d_0 conda-forge
dask 2023.1.1 pyhd8ed1ab_0 conda-forge
dask-core 2023.1.1 pyhd8ed1ab_0 conda-forge
dav1d 1.0.0 h8ffe710_1 conda-forge
debugpy 1.6.6 py39h99910a6_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
deprecated 1.2.13 pyh6c4a22f_0 conda-forge
devbio-napari 0.8.1 win_h08f2357_0 conda-forge
distributed 2023.1.1 pyhd8ed1ab_0 conda-forge
docstring_parser 0.15 pyhd8ed1ab_0 conda-forge
docutils 0.19 py39hcbf5309_1 conda-forge
eigen 3.4.0 h2d74725_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.1.0 pyhd8ed1ab_0 conda-forge
executing 1.2.0 pyhd8ed1ab_0 conda-forge
expat 2.5.0 h1537add_0 conda-forge
fasteners 0.17.3 pyhd8ed1ab_0 conda-forge
ffmpeg 5.1.2 gpl_h5b1d025_106 conda-forge
fftw 3.3.10 nompi_h38027f0_106 conda-forge
finesse 3.0a1 py39h9308f6b_1 conda-forge
flit-core 3.8.0 pyhd8ed1ab_0 conda-forge
fmt 9.1.0 h181d51b_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.14.2 hbde0cde_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.38.0 py39ha55989b_1 conda-forge
freetype 2.12.1 h546665d_1 conda-forge
freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge
fsspec 2023.1.0 pyhd8ed1ab_0 conda-forge
funcsigs 1.0.2 py_3 conda-forge
gettext 0.21.1 h5728263_0 conda-forge
giflib 5.2.1 h8d14728_2 conda-forge
glib 2.74.1 h12be248_1 conda-forge
glib-tools 2.74.1 h12be248_1 conda-forge
gst-plugins-base 1.21.3 h001b923_1 conda-forge
gstreamer 1.21.3 h6b5321d_1 conda-forge
h5py 3.8.0 nompi_py39hbc6f334_100 conda-forge
hdbscan 0.8.29 py39hc266a54_1 conda-forge
hdf5 1.12.2 nompi_h2a0e4a3_101 conda-forge
heapdict 1.0.1 py_0 conda-forge
hsluv 5.0.2 pyh44b312d_0 conda-forge
icu 70.1 h0e60522_0 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
imagecodecs 2022.9.26 py39haf5b5c4_4 conda-forge
imagecodecs-lite 2019.12.3 py39hc266a54_6 conda-forge
imageio 2.25.0 pyh24c5eb1_0 conda-forge
imageio-ffmpeg 0.4.8 pyhd8ed1ab_0 conda-forge
imagesize 1.4.1 pyhd8ed1ab_0 conda-forge
importlib-metadata 6.0.0 pyha770c72_0 conda-forge
importlib_resources 5.10.2 pyhd8ed1ab_0 conda-forge
iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge
intel-openmp 2023.0.0 h57928b3_25922 conda-forge
ipycanvas 0.13.1 pyhd8ed1ab_0 conda-forge
ipyevents 2.0.1 pyhd8ed1ab_0 conda-forge
ipykernel 6.20.2 pyh025b116_0 conda-forge
ipython 8.9.0 pyh08f2357_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 8.0.4 pyhd8ed1ab_0 conda-forge
jedi 0.18.2 pyhd8ed1ab_0 conda-forge
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
joblib 1.2.0 pyhd8ed1ab_0 conda-forge
jpeg 9e h8ffe710_2 conda-forge
json5 0.9.5 pyh9f0ad1d_0 conda-forge
jsonschema 4.17.3 pyhd8ed1ab_0 conda-forge
jupyter 1.0.0 py39hcbf5309_8 conda-forge
jupyter_client 7.4.9 pyhd8ed1ab_0 conda-forge
jupyter_console 6.4.4 pyhd8ed1ab_0 conda-forge
jupyter_core 5.1.5 py39hcbf5309_0 conda-forge
jupyter_server 1.23.5 pyhd8ed1ab_0 conda-forge
jupyterlab 3.5.3 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge
jupyterlab_server 2.19.0 pyhd8ed1ab_0 conda-forge
jupyterlab_widgets 3.0.5 pyhd8ed1ab_0 conda-forge
jupytext 1.14.4 pyhcff175f_0 conda-forge
jxrlib 1.1 h8ffe710_2 conda-forge
khronos-opencl-icd-loader 2022.09.30 h64bf75a_2 conda-forge
kiwisolver 1.4.4 py39h1f6ef14_1 conda-forge
krb5 1.20.1 h6609f42_0 conda-forge
lcms2 2.14 h90d422f_0 conda-forge
lerc 4.0.0 h63175ca_0 conda-forge
libaec 1.0.6 h63175ca_1 conda-forge
libarchive 3.6.2 h62576cb_0 conda-forge
libavif 0.11.1 h8f5c5bc_0 conda-forge
libblas 3.9.0 16_win64_mkl conda-forge
libbrotlicommon 1.0.9 hcfcfb64_8 conda-forge
libbrotlidec 1.0.9 hcfcfb64_8 conda-forge
libbrotlienc 1.0.9 hcfcfb64_8 conda-forge
libcblas 3.9.0 16_win64_mkl conda-forge
libclang 15.0.7 default_h77d9078_0 conda-forge
libclang13 15.0.7 default_h77d9078_0 conda-forge
libcurl 7.87.0 h68f0423_0 conda-forge
libdeflate 1.14 hcfcfb64_0 conda-forge
libffi 3.4.2 h8ffe710_5 conda-forge
libglib 2.74.1 he8f3873_1 conda-forge
libhwloc 2.8.0 h039e092_1 conda-forge
libiconv 1.17 h8ffe710_0 conda-forge
libitk 5.3.0 h6e1890f_0 conda-forge
liblapack 3.9.0 16_win64_mkl conda-forge
liblapacke 3.9.0 16_win64_mkl conda-forge
libmamba 1.2.0 h37bf487_0 conda-forge
libmambapy 1.2.0 py39he9eb272_0 conda-forge
libogg 1.3.4 h8ffe710_1 conda-forge
libopus 1.3.1 h8ffe710_1 conda-forge
libpng 1.6.39 h19919ed_0 conda-forge
libsodium 1.0.18 h8d14728_1 conda-forge
libsolv 0.7.23 h12be248_0 conda-forge
libsqlite 3.40.0 hcfcfb64_0 conda-forge
libssh2 1.10.0 h680486a_3 conda-forge
libtiff 4.4.0 hc4f729c_5 conda-forge
libvorbis 1.3.7 h0e60522_0 conda-forge
libwebp-base 1.2.4 h8ffe710_0 conda-forge
libxcb 1.13 hcd874cb_1004 conda-forge
libxml2 2.10.3 hc3477c8_0 conda-forge
libzlib 1.2.13 hcfcfb64_4 conda-forge
libzopfli 1.0.3 h0e60522_0 conda-forge
llvmlite 0.39.1 py39hd28a505_1 conda-forge
locket 1.0.0 pyhd8ed1ab_0 conda-forge
loguru 0.6.0 py39hcbf5309_2 conda-forge
lz4 4.2.0 py39hf617134_0 conda-forge
lz4-c 1.9.4 hcfcfb64_0 conda-forge
lzo 2.10 he774522_1000 conda-forge
m2w64-gcc-libgfortran 5.3.0 6 conda-forge
m2w64-gcc-libs 5.3.0 7 conda-forge
m2w64-gcc-libs-core 5.3.0 7 conda-forge
m2w64-gmp 6.1.0 2 conda-forge
m2w64-libwinpthread-git 5.0.0.4634.697f757 2 conda-forge
magicgui 0.6.1 pyhd8ed1ab_0 conda-forge
mako 1.2.4 pyhd8ed1ab_0 conda-forge
mamba 1.2.0 py39hb3d9227_0 conda-forge
markdown-it-py 2.1.0 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.2 py39ha55989b_0 conda-forge
matplotlib-base 3.6.3 py39haf65ace_0 conda-forge
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
mdit-py-plugins 0.3.3 pyhd8ed1ab_0 conda-forge
mdurl 0.1.0 pyhd8ed1ab_0 conda-forge
menuinst 1.4.19 py39hcbf5309_1 conda-forge
mistune 2.0.4 pyhd8ed1ab_0 conda-forge
mkl 2022.1.0 h6a75c08_874 conda-forge
mpmath 1.2.1 pyhd8ed1ab_0 conda-forge
msgpack-python 1.0.4 py39h1f6ef14_1 conda-forge
msys2-conda-epoch 20160418 1 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mypy_extensions 0.4.3 py39hcbf5309_6 conda-forge
napari 0.4.16 pyh275ddea_0_pyqt conda-forge
napari-3d-ortho-viewer 0.0.1 pyhd8ed1ab_0 conda-forge
napari-accelerated-pixel-and-object-classification 0.12.3 pyhd8ed1ab_0 conda-forge
napari-animation 0.0.5 pyhd8ed1ab_0 conda-forge
napari-assistant 0.4.4 pyhd8ed1ab_0 conda-forge
napari-blob-detection 0.0.2 pyhd8ed1ab_0 conda-forge
napari-brightness-contrast 0.1.8 pyhd8ed1ab_0 conda-forge
napari-clusters-plotter 0.6.0 pyhd8ed1ab_0 conda-forge
napari-console 0.0.7 pyhd8ed1ab_0 conda-forge
napari-crop 0.1.6 pyhd8ed1ab_0 conda-forge
napari-curtain 0.1.1 pyhd8ed1ab_0 conda-forge
napari-czifile2 0.2.7 pyhd8ed1ab_0 conda-forge
napari-folder-browser 0.1.3 pyhd8ed1ab_0 conda-forge
napari-layer-details-display 0.1.4 pyhd8ed1ab_0 conda-forge
napari-mouse-controls 0.1.3 pyhd8ed1ab_0 conda-forge
napari-plot-profile 0.2.2 pyhd8ed1ab_0 conda-forge
napari-plugin-engine 0.2.0 pyhd8ed1ab_2 conda-forge
napari-plugin-search 0.1.3 pyhd8ed1ab_0 conda-forge
napari-pyclesperanto-assistant 0.22.0 pyhd8ed1ab_0 conda-forge
napari-pystackreg 0.1.4 pyhd8ed1ab_0 conda-forge
napari-roi 0.1.7 pyhd8ed1ab_0 conda-forge
napari-segment-blobs-and-things-with-membranes 0.3.3 pyhd8ed1ab_0 conda-forge
napari-simpleitk-image-processing 0.4.5 pyhd8ed1ab_0 conda-forge
napari-skimage-regionprops 0.8.0 pyhd8ed1ab_0 conda-forge
napari-svg 0.1.6 pyhd8ed1ab_1 conda-forge
napari-tabu 0.1.5 pyhd8ed1ab_0 conda-forge
napari-time-slicer 0.4.9 pyhd8ed1ab_1 conda-forge
napari-tools-menu 0.1.18 pyhd8ed1ab_0 conda-forge
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napari-workflow-optimizer 0.1.4 pyhd8ed1ab_0 conda-forge
napari-workflows 0.2.8 pyhd8ed1ab_0 conda-forge
nbclassic 0.4.8 pyhd8ed1ab_0 conda-forge
nbclient 0.7.2 pyhd8ed1ab_0 conda-forge
nbconvert 7.2.9 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.2.9 pyhd8ed1ab_0 conda-forge
nbconvert-pandoc 7.2.9 pyhd8ed1ab_0 conda-forge
nbformat 5.7.3 pyhd8ed1ab_0 conda-forge
nest-asyncio 1.5.6 pyhd8ed1ab_0 conda-forge
networkx 3.0 pyhd8ed1ab_0 conda-forge
notebook 6.5.2 pyha770c72_1 conda-forge
notebook-shim 0.2.2 pyhd8ed1ab_0 conda-forge
npe2 0.6.1 pyhd8ed1ab_1 conda-forge
numba 0.56.4 py39h99ae161_0 conda-forge
numcodecs 0.11.0 py39h99910a6_1 conda-forge
numpy 1.23.5 py39hbccbffa_0 conda-forge
numpydoc 1.5.0 pyhd8ed1ab_0 conda-forge
openh264 2.3.1 h63175ca_1 conda-forge
openjpeg 2.5.0 hc9384bd_1 conda-forge
openssl 1.1.1s hcfcfb64_1 conda-forge
packaging 23.0 pyhd8ed1ab_0 conda-forge
pandas 1.5.3 py39h2ba5b7c_0 conda-forge
pandoc 2.19.2 h57928b3_1 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
partd 1.3.0 pyhd8ed1ab_0 conda-forge
pcre2 10.40 h17e33f8_0 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 9.2.0 py39h595c93f_3 conda-forge
pint 0.20.1 pyhd8ed1ab_0 conda-forge
pip 22.3.1 py39haa95532_0
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge
platformdirs 2.6.2 pyhd8ed1ab_0 conda-forge
platymatch 0.0.3 pyhd8ed1ab_0 conda-forge
pluggy 1.0.0 pyhd8ed1ab_5 conda-forge
ply 3.11 py_1 conda-forge
pooch 1.6.0 pyhd8ed1ab_0 conda-forge
prometheus_client 0.16.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.36 pyha770c72_0 conda-forge
prompt_toolkit 3.0.36 hd8ed1ab_0 conda-forge
psutil 5.9.4 py39ha55989b_0 conda-forge
psygnal 0.7.0 pyhd8ed1ab_0 conda-forge
pthread-stubs 0.4 hcd874cb_1001 conda-forge
pthreads-win32 2.9.1 hfa6e2cd_3 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
pybind11-abi 4 hd8ed1ab_3 conda-forge
pyclesperanto-prototype 0.22.0 pyhd8ed1ab_0 conda-forge
pycodestyle 2.10.0 pyhd8ed1ab_0 conda-forge
pycosat 0.6.4 py39ha55989b_1 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pydantic 1.10.4 py39ha55989b_1 conda-forge
pygments 2.14.0 pyhd8ed1ab_0 conda-forge
pynndescent 0.5.8 pyh1a96a4e_0 conda-forge
pyopencl 2022.3.1 py39he9b43b8_0 conda-forge
pyopengl 3.1.6 pyhd8ed1ab_1 conda-forge
pyopenssl 23.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge
pyperclip 1.8.2 pyhd8ed1ab_2 conda-forge
pyproject_hooks 1.0.0 pyhd8ed1ab_0 conda-forge
pyqt 5.15.7 py39hb77abff_3 conda-forge
pyqt5-sip 12.11.0 py39h99910a6_3 conda-forge
pyqtgraph 0.13.1 pyhd8ed1ab_1 conda-forge
pyrsistent 0.19.3 py39ha55989b_0 conda-forge
pysocks 1.7.1 pyh0701188_6 conda-forge
pystackreg 0.2.7 py39h2ba5b7c_1 conda-forge
pytest 7.2.1 pyhd8ed1ab_0 conda-forge
python 3.9.16 h6244533_0
python-build 0.10.0 pyhd8ed1ab_0 conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.16.2 pyhd8ed1ab_0 conda-forge
python_abi 3.9 2_cp39 conda-forge
pytomlpp 1.0.11 py39h1f6ef14_1 conda-forge
pytools 2022.1.14 pyhd8ed1ab_0 conda-forge
pytz 2022.7.1 pyhd8ed1ab_0 conda-forge
pywavelets 1.4.1 py39hc266a54_0 conda-forge
pywin32 304 py39h99910a6_2 conda-forge
pywinpty 2.0.10 py39h99910a6_0 conda-forge
pyyaml 6.0 py39ha55989b_5 conda-forge
pyzmq 25.0.0 py39hea35a22_0 conda-forge
qt-main 5.15.6 h068e40c_6 conda-forge
qtconsole 5.4.0 pyhd8ed1ab_0 conda-forge
qtconsole-base 5.4.0 pyha770c72_0 conda-forge
qtpy 2.3.0 pyhd8ed1ab_0 conda-forge
redlionfish 0.8 py39hcbf5309_2 conda-forge
reikna 0.8.0 pyhd8ed1ab_0 conda-forge
reproc 14.2.4 hcfcfb64_0 conda-forge
reproc-cpp 14.2.4 h63175ca_0 conda-forge
requests 2.28.2 pyhd8ed1ab_0 conda-forge
rich 13.3.1 pyhd8ed1ab_1 conda-forge
ruamel.yaml 0.17.21 py39ha55989b_2 conda-forge
ruamel.yaml.clib 0.2.7 py39ha55989b_1 conda-forge
scikit-image 0.19.3 py39h2ba5b7c_2 conda-forge
scikit-learn 1.2.1 py39h6fe01c0_0 conda-forge
scipy 1.10.0 py39hfbf2dce_0 conda-forge
send2trash 1.8.0 pyhd8ed1ab_0 conda-forge
setuptools 65.6.3 py39haa95532_0
shellingham 1.5.0.post1 pyhd8ed1ab_0 conda-forge
simpleitk 2.2.1 py39h138a4a7_1 conda-forge
sip 6.7.6 py39h99910a6_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sly 0.4 pyhd8ed1ab_0 conda-forge
snappy 1.1.9 hfb803bf_2 conda-forge
sniffio 1.3.0 pyhd8ed1ab_0 conda-forge
snowballstemmer 2.2.0 pyhd8ed1ab_0 conda-forge
sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge
sphinx 6.1.3 pyhd8ed1ab_0 conda-forge
sphinxcontrib-applehelp 1.0.4 pyhd8ed1ab_0 conda-forge
sphinxcontrib-devhelp 1.0.2 py_0 conda-forge
sphinxcontrib-htmlhelp 2.0.0 pyhd8ed1ab_0 conda-forge
sphinxcontrib-jsmath 1.0.1 py_0 conda-forge
sphinxcontrib-qthelp 1.0.3 py_0 conda-forge
sphinxcontrib-serializinghtml 1.1.5 pyhd8ed1ab_2 conda-forge
sqlite 3.40.1 h2bbff1b_0
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
stackview 0.5.2 pyhd8ed1ab_0 conda-forge
suitesparse 5.4.0 h5d0cbe0_1 conda-forge
superqt 0.4.1 pyhd8ed1ab_0 conda-forge
svt-av1 1.4.1 h63175ca_0 conda-forge
sympy 1.11.1 py39hcbf5309_2 conda-forge
tabulate 0.9.0 pyhd8ed1ab_1 conda-forge
tbb 2021.7.0 h91493d7_1 conda-forge
tblib 1.7.0 pyhd8ed1ab_0 conda-forge
terminado 0.17.0 pyh08f2357_0 conda-forge
the-segmentation-game 0.2.0 pyhd8ed1ab_0 conda-forge
threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge
tifffile 2022.10.10 pyhd8ed1ab_0 conda-forge
tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h8ffe710_0 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
toolz 0.12.0 pyhd8ed1ab_0 conda-forge
tornado 6.2 py39ha55989b_1 conda-forge
tqdm 4.64.1 pyhd8ed1ab_0 conda-forge
traitlets 5.8.1 pyhd8ed1ab_0 conda-forge
transforms3d 0.4.1 pyhd8ed1ab_0 conda-forge
typer 0.4.2 pyhd8ed1ab_0 conda-forge
typing-extensions 4.4.0 hd8ed1ab_0 conda-forge
typing_extensions 4.4.0 pyha770c72_0 conda-forge
tzdata 2022g h04d1e81_0
ucrt 10.0.22621.0 h57928b3_0 conda-forge
umap-learn 0.5.3 py39hcbf5309_0 conda-forge
unicodedata2 15.0.0 py39ha55989b_0 conda-forge
urllib3 1.26.14 pyhd8ed1ab_0 conda-forge
vc 14.2 h21ff451_1
vispy 0.10.0 py39h5d4886f_0 conda-forge
vs2015_runtime 14.34.31931 h4c5c07a_10 conda-forge
wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 py_1 conda-forge
websocket-client 1.5.0 pyhd8ed1ab_0 conda-forge
wheel 0.37.1 pyhd3eb1b0_0
widgetsnbextension 4.0.5 pyhd8ed1ab_0 conda-forge
win32_setctime 1.1.0 pyhd8ed1ab_0 conda-forge
win_inet_pton 1.1.0 pyhd8ed1ab_6 conda-forge
wincertstore 0.2 py39haa95532_2
winpty 0.4.3 4 conda-forge
wrapt 1.14.1 py39ha55989b_1 conda-forge
x264 1!164.3095 h8ffe710_2 conda-forge
x265 3.5 h2d74725_3 conda-forge
xorg-libxau 1.0.9 hcd874cb_0 conda-forge
xorg-libxdmcp 1.1.3 hcd874cb_0 conda-forge
xz 5.2.6 h8d14728_0 conda-forge
yaml 0.2.5 h8ffe710_2 conda-forge
yaml-cpp 0.7.0 h63175ca_2 conda-forge
zarr 2.13.3 pyhd8ed1ab_0 conda-forge
zeromq 4.3.4 h0e60522_1 conda-forge
zfp 1.0.0 h63175ca_3 conda-forge
zict 2.2.0 pyhd8ed1ab_0 conda-forge
zipp 3.12.0 pyhd8ed1ab_0 conda-forge
zlib-ng 2.0.6 h8ffe710_0 conda-forge
zstandard 0.19.0 py39h95af829_1 conda-forge
zstd 1.5.2 h12be248_6 conda-forge
I just noticed that you are using 0.5 in x and y.
I tested to load using scale = [1,0.5,0.5]
and I get these results :
-
It seems the z is ok now:
-
but the result is much bigger in xy !!!
