Voxel size of output-layer is different from input layer

[haesleinhuepf]

reported here: https://forum.image.sc/t/napari-accelerated-pixel-object-classification-apoc-output-scale-input-loading/77106

[haesleinhuepf]

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

[romainGuiet]

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
napari-workflow-inspector 0.2.2              pyhd8ed1ab_0    conda-forge
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
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pyyaml                    6.0              py39ha55989b_5    conda-forge
pyzmq                     25.0.0           py39hea35a22_0    conda-forge
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qtpy                      2.3.0              pyhd8ed1ab_0    conda-forge
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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
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sympy                     1.11.1           py39hcbf5309_2    conda-forge
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tblib                     1.7.0              pyhd8ed1ab_0    conda-forge
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tifffile                  2022.10.10         pyhd8ed1ab_0    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h8ffe710_0    conda-forge
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tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
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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
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websocket-client          1.5.0              pyhd8ed1ab_0    conda-forge
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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

[romainGuiet]

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 !!!