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update pyclesperanto dependency #117

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update pyclesperanto dependency #117

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2 changes: 1 addition & 1 deletion conda/napari_CellSeg3D_ARM64.yml
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Expand Up @@ -18,7 +18,7 @@ dependencies:
- monai[nibabel, einops]>=0.9.0
- tqdm
- scikit-image
- pyclesperanto-prototype
- pyclesperanto
- tqdm
- matplotlib
- napari_cellseg3d
2 changes: 1 addition & 1 deletion docs/welcome.rst
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Expand Up @@ -168,7 +168,7 @@ This plugin additionally uses the following libraries and software:
.. _PyTorch: https://pytorch.org/
.. _MONAI project: https://monai.io/
.. _on their website: https://docs.monai.io/en/stable/networks.html#nets
.. _pyclEsperanto: https://github.com/clEsperanto/pyclesperanto_prototype
.. _pyclEsperanto: https://github.com/clEsperanto/pyclesperanto
.. _WNet: https://arxiv.org/abs/1711.08506

.. rubric:: References
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4 changes: 2 additions & 2 deletions napari_cellseg3d/code_models/instance_segmentation.py
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Expand Up @@ -6,7 +6,7 @@
from typing import List

import numpy as np
import pyclesperanto_prototype as cle
import pyclesperanto as cle
from qtpy.QtWidgets import QWidget
from skimage.measure import label, regionprops
from skimage.morphology import remove_small_objects
Expand Down Expand Up @@ -287,7 +287,7 @@ def voronoi_otsu(
BASED ON CODE FROM : napari_pyclesperanto_assistant by Robert Haase
https://github.com/clEsperanto/napari_pyclesperanto_assistant
Original code at :
https://github.com/clEsperanto/pyclesperanto_prototype/blob/master/pyclesperanto_prototype/_tier9/_voronoi_otsu_labeling.py.
https://github.com/clEsperanto/pyclesperanto/blob/d1990e28b1da44a7921890b7bd809d522d3198b8/pyclesperanto/_tier7.py#L409-L448.

Args:
volume (np.ndarray): volume to segment
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2 changes: 1 addition & 1 deletion napari_cellseg3d/dev_scripts/sliding_window_voronoi.py
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@@ -1,6 +1,6 @@
"""Test script for sliding window Voronoi-Otsu segmentation.""."""
import numpy as np
import pyclesperanto_prototype as cle
import pyclesperanto as cle
from tqdm import tqdm


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402 changes: 201 additions & 201 deletions notebooks/Colab_inference_demo.ipynb
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2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -42,7 +42,7 @@ dependencies = [
"tqdm",
# "nibabel",
# "pillow",
"pyclesperanto-prototype",
"pyclesperanto",
"tqdm",
"matplotlib",
"pydensecrf2",
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2 changes: 1 addition & 1 deletion requirements.txt
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Expand Up @@ -13,7 +13,7 @@ napari[all]>=0.4.14
QtPy
opencv-python>=4.5.5
pre-commit
pyclesperanto-prototype>=0.22.0
pyclesperanto>=0.18.3
matplotlib>=3.4.1
ruff
tifffile>=2022.2.9
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2 changes: 1 addition & 1 deletion setup.cfg
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Expand Up @@ -24,7 +24,7 @@ install_requires =
itk
tqdm
nibabel
pyclesperanto-prototype
pyclesperanto
scikit-image
pillow
tqdm
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