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@@ -0,0 +1 @@ +/pyclesperanto_prototype-0.24.1.tar.gz diff --git a/python-pyclesperanto-prototype.spec b/python-pyclesperanto-prototype.spec new file mode 100644 index 0000000..726d90c --- /dev/null +++ b/python-pyclesperanto-prototype.spec @@ -0,0 +1,1728 @@ +%global _empty_manifest_terminate_build 0 +Name: python-pyclesperanto-prototype +Version: 0.24.1 +Release: 1 +Summary: GPU-accelerated image processing in python using OpenCL +License: BSD-3-Clause +URL: https://github.com/clEsperanto/pyclesperanto_prototype +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/ae/5e/713a9e6ab51e99ce555e153285a0f38a3edfe518ff553460282065df70fa/pyclesperanto_prototype-0.24.1.tar.gz +BuildArch: noarch + +Requires: python3-numpy +Requires: python3-pyopencl +Requires: python3-toolz +Requires: python3-scikit-image +Requires: python3-matplotlib +Requires: python3-transforms3d + +%description +# py-clesperanto
+[](https://forum.image.sc/tag/clesperanto)
+[](http://clesperanto.net)
+[](https://pypi.org/project/pyclesperanto-prototype)
+[](https://anaconda.org/conda-forge/pyclesperanto-prototype)
+[](https://github.com/clEsperanto/pyclesperanto_prototype/graphs/contributors)
+[](https://pypistats.org/packages/pyclesperanto_prototype)
+[](https://github.com/clEsperanto/pyclesperanto_prototype/)
+[](https://github.com/clEsperanto/pyclesperanto_prototype/)
+[](https://github.com/haesleinhuepf/pyclesperanto_prototype/raw/master/LICENSE)
+[](https://python.org)
+[](https://github.com/clesperanto/pyclesperanto_prototype/actions)
+[](https://codecov.io/gh/clesperanto/pyclesperanto_prototype)
+[](https://en.wikipedia.org/wiki/Software_release_life_cycle#Alpha)
+[](https://zenodo.org/badge/latestdoi/248206619)
+
+py-clesperanto is a prototype for [clesperanto](http://clesperanto.net) - a multi-platform multi-language framework for GPU-accelerated image processing.
+We mostly use it in the life sciences for analysing 3- and 4-dimensional microsopy data, e.g. as we face it developmental biology when segmenting cells and studying
+their individual properties as well as properties of compounds of cells forming tissues.
+
+
+Image data source: Daniela Vorkel, Myers lab, MPI-CBG, rendered using [napari](https://github.com/napari/napari)
+
+clesperanto uses [OpenCL kernels](https://github.com/clEsperanto/clij-opencl-kernels/tree/development/src/main/java/net/haesleinhuepf/clij/kernels) from [CLIJ](http://clij.github.io/).
+
+For users convenience, there are code generators available for [napari](https://clesperanto.github.io/napari_pyclesperanto_assistant/) and [Fiji](https://clij.github.io/assistant/).
+Also check out the [napari workflow optimizer](https://github.com/haesleinhuepf/napari-workflow-optimizer) for semi-automatic parameter tuning of clesperanto-functions.
+
+## Reference
+The preliminary API reference is available [here](https://clesperanto.github.io/pyclesperanto_prototype/docs/_build/html/).
+Furthermore, parts of the [reference](https://clij.github.io/clij2-docs/reference__pyclesperanto) are also available within the CLIJ2 documentation.
+
+## Installation
+* Get a conda/python environment, e.g. via [mamba-forge](https://github.com/conda-forge/miniforge#mambaforge).
+* If you never used python/conda environments before, please follow [these instructions](https://biapol.github.io/blog/mara_lampert/getting_started_with_mambaforge_and_python/readme.html) first.
+
+```
+conda create --name cle_39 python=3.9
+conda activate cle_39
+```
+
+* Install pyclesperanto-prototype using [mamba / conda](https://focalplane.biologists.com/2022/12/08/managing-scientific-python-environments-using-conda-mamba-and-friends/):
+
+```
+mamba install -c conda-forge pyclesperanto-prototype
+```
+
+OR using pip:
+
+```
+pip install pyclesperanto-prototype
+```
+
+## Troubleshooting: Graphics cards drivers
+
+In case error messages contains "ImportError: DLL load failed while importing cl: The specified procedure could not be found" [see also](https://github.com/clEsperanto/pyclesperanto_prototype/issues/55) or "clGetPlatformIDs failed: PLATFORM_NOT_FOUND_KHR", please install recent drivers for your graphics card and/or OpenCL device. Select the right driver source depending on your hardware from this list:
+
+* [AMD drivers](https://www.amd.com/en/support)
+* [NVidia drivers](https://www.nvidia.com/download/index.aspx)
+* [Intel GPU drivers](https://www.intel.com/content/www/us/en/download/726609/intel-arc-graphics-windows-dch-driver.html)
+* [Microsoft Windows OpenCL support](https://www.microsoft.com/en-us/p/opencl-and-opengl-compatibility-pack/9nqpsl29bfff)
+
+Sometimes, mac-users need to install this:
+
+ mamba install -c conda-forge ocl_icd_wrapper_apple
+
+Sometimes, linux users need to install this:
+
+ mamba install -c conda-forge ocl-icd-system
+
+## Computing on Central Processing units (CPUs)
+
+If no OpenCL-compatible GPU is available, pyclesperanto-prototype can make use of CPUs instead.
+Just install [oclgrind](https://github.com/jrprice/Oclgrind)
+or [pocl](http://portablecl.org/), e.g. using mamba / conda. Oclgrind is recommended for Windows systems, PoCL for Linux. MacOS typically comes with OpenCL support for CPUs.
+
+```
+mamba install oclgrind -c conda-forge
+```
+
+OR
+
+```
+mamba install pocl -c conda-forge
+```
+
+Owners of compatible Intel Xeon CPUs can also install a driver to use them for computing:
+* [Intel CPU OpenCL drivers](https://www.intel.com/content/www/us/en/developer/articles/tool/opencl-drivers.html#latest_CPU_runtime)
+
+
+## Example code
+A basic image processing workflow loads blobs.gif and counts the number of objects:
+
+```python
+import pyclesperanto_prototype as cle
+
+from skimage.io import imread, imsave
+
+# initialize / select GPU with "TX" in their name
+device = cle.select_device("TX")
+print("Used GPU: ", device)
+
+# load data
+image = imread('https://imagej.nih.gov/ij/images/blobs.gif')
+
+# process the image
+inverted = cle.subtract_image_from_scalar(image, scalar=255)
+blurred = cle.gaussian_blur(inverted, sigma_x=1, sigma_y=1)
+binary = cle.threshold_otsu(blurred)
+labeled = cle.connected_components_labeling_box(binary)
+
+# The maximium intensity in a label image corresponds to the number of objects
+num_labels = labeled.max()
+print(f"Number of objects in the image: {num_labels}")
+
+# save image to disc
+imsave("result.tif", labeled)
+```
+
+## Example gallery
+
+<table border="0">
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_select_GPU.png" width="300"/>
+
+</td><td>
+
+[Select GPU](https://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/select_GPU.py)
+
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/jupyter.png" width="300"/>
+
+</td><td>
+
+[Image processing in Jupyter Notebooks](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/interoperability/jupyter.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_count_blobs.png" width="300"/>
+
+</td><td>
+
+[Counting blobs](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/count_blobs.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/voronoi_otsu_labeling.png" width="300"/>
+
+</td><td>
+
+[Voronoi-Otsu labeling](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/segmentation/voronoi_otsu_labeling.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/segmentation_3d.png" width="300"/>
+
+</td><td>
+
+[3D Image segmentation ](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/segmentation/Segmentation_3D.ipynb)
+
+</td></tr>
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/segmentation_2d_membranes.png" width="300"/>
+
+</td><td>
+
+[Cell segmentation based on membranes](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/segmentation/segmentation_2d_membranes.ipynb)
+
+</td></tr>
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/counting_nuclei_multichannel.png" width="300"/>
+
+</td><td>
+
+[Counting nuclei according to expression in multiple channels](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/measurement/counting_nuclei_multichannel.ipynb)
+
+</td></tr>
+
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/differentiate_nuclei_intensity.png" width="300"/>
+
+</td><td>
+
+[Differentiating nuclei according to signal intensity](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/measurement/differentiate_nuclei_intensity.ipynb)
+
+</td></tr>
+
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/bead_segmentation.png" width="300"/>
+
+</td><td>
+
+[Detecting beads and measuring their size](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/segmentation/bead_segmentation.ipynb)
+
+</td></tr>
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/label_statistics.png" width="300"/>
+
+</td><td>
+
+[Label statistics](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/label_statistics.ipynb)
+
+</td></tr>
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/parametric_maps.png" width="300"/>
+
+</td><td>
+
+[Parametric maps](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/tissues/parametric_maps.ipynb)
+
+</td></tr>
+
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/intensities_along_lines.png" width="300"/>
+
+</td><td>
+
+[Measure intensity along lines](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/measurement/intensities_along_lines.ipynb)
+
+</td></tr>
+
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_crop_and_paste_images.png" width="300"/>
+
+</td><td>
+
+[Crop and paste images](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/crop_and_paste_images.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_inspecting_3d_images.png" width="300"/>
+
+</td><td>
+
+[Inspecting 3D image data](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/inspecting_3d_images.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_affine_transforms.png" width="300"/>
+
+</td><td>
+
+[Rotation, scaling, translation, affine transforms](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/transforms/affine_transforms.ipynb)
+
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_deskew.png" width="300"/>
+
+</td><td>
+
+[Deskewing](https://github.com/clEsperanto/pyclesperanto_prototype/blob/master/demo/transforms/deskew.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_multiply_vectors_and_matrices.png" width="300"/>
+
+</td><td>
+
+[Multiply vectors and matrices](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/multiply_vectors_and_matrices.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_multiply_matrices.png" width="300"/>
+
+</td><td>
+
+[Matrix multiplication](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/multiply_matrices.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_spots_pointlists_matrices_tables.png" width="300"/>
+
+</td><td>
+
+* [Working with spots, pointlist and matrices](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/spots_pointlists_matrices_tables.ipynb)
+* [Lists of nonzero pixel coordinates](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/nonzero.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/mesh_between_centroids.png" width="300"/>
+
+</td><td>
+
+[Mesh between centroids](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/mesh_between_centroids.ipynb)
+
+</td></tr><tr><td>
+
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/mesh_between_touching_neighbors.png" width="300"/>
+
+</td><td>
+
+[Mesh between touching neighbors](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/mesh_between_touching_neighbors.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/mesh_with_distances.png" width="300"/>
+
+</td><td>
+
+[Mesh with distances](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/mesh_with_distances.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/mesh_nearest_neighbors.png" width="300"/>
+
+</td><td>
+
+[Mesh nearest_neighbors](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/mesh_nearest_neighbors.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/ipgraph_networkx.png" width="300"/>
+
+</td><td>
+
+[Export to igraph and networkx](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/ipgraph_networkx.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/neighborhood_definitions.png" width="300"/>
+
+</td><td>
+
+[Neighborhood definitions](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/neighborhood_definitions.ipynb)
+
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/tissue_neighborhood_quantification.png" width="300"/>
+
+</td><td>
+
+[Tissue neighborhood quantification](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/tissues/tissue_neighborhood_quantification.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/neighbors_of_neighbors.png" width="300"/>
+
+</td><td>
+
+[Neighbors of neighbors](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/neighbors_of_neighbors.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_voronoi_diagrams.png" width="300"/>
+
+</td><td>
+
+[Voronoi diagrams](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/voronoi_diagrams.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/shape_descriptors_based_on_neighborhood_graphs.png" width="300"/>
+
+</td><td>
+
+[Shape descriptors based on neighborhood graphs](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/shape_descriptors_based_on_neighborhood_graphs.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/distance_to_other_labels.png" width="300"/>
+
+</td><td>
+
+[Measuring distances between labels in two label images](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/distance_to_other_labels.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_tribolium_napari.png" width="300"/>
+
+</td><td>
+
+[Tribolium morphometry + Napari](https://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/tribolium_morphometry/tribolium.py)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_tribolium_morphometry.png" width="300"/>
+
+</td><td>
+
+[Tribolium morphometry](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/tribolium_morphometry/tribolium_morphometry2.ipynb)
+[(archived version)](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/tribolium_morphometry/tribolium_morphometry.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_napari_dask.png" width="300"/>
+
+</td><td>
+
+[napari+dask timelapse processing](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/napari_gui/napari_dask.ipynb)
+
+</td></tr>
+</table>
+
+## Technical insights
+
+<table border="0"><tr><td>
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/browse_operations.png" width="300"/>
+
+</td><td>
+
+[Browsing operations](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/browse_operations.ipynb)
+
+</td></tr>
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/interactive_widgets.gif" width="300"/>
+
+</td><td>
+
+[Interactive widgets](https://colab.research.google.com/github/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/browse_operations.ipynb)
+
+</td></tr>
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/optimize_blobs_segmentation.png" width="300"/>
+
+</td><td>
+
+[Automatic workflow optimization](https://colab.research.google.com/github/clEsperanto/pyclesperanto_prototype/tree/master/demo/optimization/optimize_blobs_segmentation.ipynb)
+
+</td></tr>
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/memory_management.png" width="300"/>
+
+</td><td>
+
+[Tracing memory consumtion on NVidia GPUs](https://github.com/clEsperanto/pyclesperanto_prototype/blob/master/demo/optimization/memory_management.ipynb)
+
+</td></tr>
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/switching_gpus.png" width="300"/>
+
+</td><td>
+
+[Exploring and switching between GPUs](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/switching_gpus.ipynb)
+
+</td></tr>
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/cupy_compatibility.png" width="300"/>
+
+</td><td>
+
+[Interoperability with cupy](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/interoperability_cupy.ipynb)
+
+[Using the cupy backend](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/select_backend.ipynb)
+
+</td></tr>
+<tr><td>
+
+<img src="./docs/images/dask.jpg" width="300"/>
+
+</td><td>
+
+[Big data handling with Dask GPU clusters](./demo/interoperability/dask.ipynb)
+
+
+</td></tr>
+</table>
+
+## Related projects
+
+<table border="0"><tr><td>
+
+<img src="https://github.com/clesperanto/napari_pyclesperanto_assistant/raw/master/docs/images/screenshot.png" width="300"/>
+
+</td><td>
+
+[napari-pyclesperanto-assistant](https://github.com/clesperanto/napari_pyclesperanto_assistant):
+A graphical user interface for general purpose GPU-accelerated image processing and analysis in napari.
+
+</td></tr><tr><td>
+
+<img src="https://github.com/haesleinhuepf/napari-accelerated-pixel-and-object-classification/raw/main/images/screenshot.png" width="300"/>
+
+</td><td>
+
+[napari-accelerated-pixel-and-object-classification](https://github.com/haesleinhuepf/napari-accelerated-pixel-and-object-classification):
+GPU-accelerated Random Forest Classifiers for pixel and labeled object classification
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/napari-clusters-plotter.png" width="300"/>
+
+</td><td>
+
+[napari-clusters-plotter](https://github.com/BiAPoL/napari-clusters-plotter):
+Clustering of objects according to their quantitative properties
+
+</td></tr></table>
+
+## Benchmarking
+We implemented some basic benchmarking notebooks allowing to see performance differences between pyclesperanto and
+some other image processing libraries, typically using the CPU. Such benchmarking results vary heavily depending on
+image size, kernel size, used operations, parameters and used hardware. Feel free to use those notebooks, adapt them to
+your use-case scenario and benchmark on your target hardware. If you have different scenarios or use-cases, you are very
+welcome to submit your notebook as pull-request!
+
+* [Affine transforms](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/affine_transforms.ipynb)
+* [Background subtraction](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/top_hat.ipynb)
+* [Gaussian blur](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/gaussian_blur.ipynb)
+* [Convolution](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/convolution.ipynb)
+* [Otsu's thresholding](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/threshold_otsu.ipynb)
+* [Connected component labeling](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/connected_component_labeling.ipynb)
+* [Extend labels](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/extend_labels.ipynb)
+* [Statistics of labeled pixels / regionprops](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/statistics_of_labeled_pixels.ipynb)
+* [Histograms](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/histograms.ipynb)
+* [Matrix multiplication](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/matrix_multiplication.ipynb)
+* [Pixel-wise comparison](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/pixelwise_comparison.ipynb)
+* [Intensity projections](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/intensity_projections.ipynb)
+* [Axis transposition](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/transpose.ipynb)
+* [Nonzero](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/nonzero.ipynb)
+
+## See also
+There are other libraries for code acceleration and GPU-acceleration for image processing.
+* [numba](https://numba.pydata.org/)
+* [cupy](https://cupy.dev)
+* [cucim](https://github.com/rapidsai/cucim)
+* [clij](https://clij.github.io)
+
+## Feedback welcome!
+clesperanto is developed in the open because we believe in the open source community. See our [community guidelines](https://clij.github.io/clij2-docs/community_guidelines). Feel free to drop feedback as [github issue](https://github.com/clEsperanto/pyclesperanto_prototype/issues) or via [image.sc](https://image.sc)
+ + +%package -n python3-pyclesperanto-prototype +Summary: GPU-accelerated image processing in python using OpenCL +Provides: python-pyclesperanto-prototype +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-pyclesperanto-prototype +# py-clesperanto
+[](https://forum.image.sc/tag/clesperanto)
+[](http://clesperanto.net)
+[](https://pypi.org/project/pyclesperanto-prototype)
+[](https://anaconda.org/conda-forge/pyclesperanto-prototype)
+[](https://github.com/clEsperanto/pyclesperanto_prototype/graphs/contributors)
+[](https://pypistats.org/packages/pyclesperanto_prototype)
+[](https://github.com/clEsperanto/pyclesperanto_prototype/)
+[](https://github.com/clEsperanto/pyclesperanto_prototype/)
+[](https://github.com/haesleinhuepf/pyclesperanto_prototype/raw/master/LICENSE)
+[](https://python.org)
+[](https://github.com/clesperanto/pyclesperanto_prototype/actions)
+[](https://codecov.io/gh/clesperanto/pyclesperanto_prototype)
+[](https://en.wikipedia.org/wiki/Software_release_life_cycle#Alpha)
+[](https://zenodo.org/badge/latestdoi/248206619)
+
+py-clesperanto is a prototype for [clesperanto](http://clesperanto.net) - a multi-platform multi-language framework for GPU-accelerated image processing.
+We mostly use it in the life sciences for analysing 3- and 4-dimensional microsopy data, e.g. as we face it developmental biology when segmenting cells and studying
+their individual properties as well as properties of compounds of cells forming tissues.
+
+
+Image data source: Daniela Vorkel, Myers lab, MPI-CBG, rendered using [napari](https://github.com/napari/napari)
+
+clesperanto uses [OpenCL kernels](https://github.com/clEsperanto/clij-opencl-kernels/tree/development/src/main/java/net/haesleinhuepf/clij/kernels) from [CLIJ](http://clij.github.io/).
+
+For users convenience, there are code generators available for [napari](https://clesperanto.github.io/napari_pyclesperanto_assistant/) and [Fiji](https://clij.github.io/assistant/).
+Also check out the [napari workflow optimizer](https://github.com/haesleinhuepf/napari-workflow-optimizer) for semi-automatic parameter tuning of clesperanto-functions.
+
+## Reference
+The preliminary API reference is available [here](https://clesperanto.github.io/pyclesperanto_prototype/docs/_build/html/).
+Furthermore, parts of the [reference](https://clij.github.io/clij2-docs/reference__pyclesperanto) are also available within the CLIJ2 documentation.
+
+## Installation
+* Get a conda/python environment, e.g. via [mamba-forge](https://github.com/conda-forge/miniforge#mambaforge).
+* If you never used python/conda environments before, please follow [these instructions](https://biapol.github.io/blog/mara_lampert/getting_started_with_mambaforge_and_python/readme.html) first.
+
+```
+conda create --name cle_39 python=3.9
+conda activate cle_39
+```
+
+* Install pyclesperanto-prototype using [mamba / conda](https://focalplane.biologists.com/2022/12/08/managing-scientific-python-environments-using-conda-mamba-and-friends/):
+
+```
+mamba install -c conda-forge pyclesperanto-prototype
+```
+
+OR using pip:
+
+```
+pip install pyclesperanto-prototype
+```
+
+## Troubleshooting: Graphics cards drivers
+
+In case error messages contains "ImportError: DLL load failed while importing cl: The specified procedure could not be found" [see also](https://github.com/clEsperanto/pyclesperanto_prototype/issues/55) or "clGetPlatformIDs failed: PLATFORM_NOT_FOUND_KHR", please install recent drivers for your graphics card and/or OpenCL device. Select the right driver source depending on your hardware from this list:
+
+* [AMD drivers](https://www.amd.com/en/support)
+* [NVidia drivers](https://www.nvidia.com/download/index.aspx)
+* [Intel GPU drivers](https://www.intel.com/content/www/us/en/download/726609/intel-arc-graphics-windows-dch-driver.html)
+* [Microsoft Windows OpenCL support](https://www.microsoft.com/en-us/p/opencl-and-opengl-compatibility-pack/9nqpsl29bfff)
+
+Sometimes, mac-users need to install this:
+
+ mamba install -c conda-forge ocl_icd_wrapper_apple
+
+Sometimes, linux users need to install this:
+
+ mamba install -c conda-forge ocl-icd-system
+
+## Computing on Central Processing units (CPUs)
+
+If no OpenCL-compatible GPU is available, pyclesperanto-prototype can make use of CPUs instead.
+Just install [oclgrind](https://github.com/jrprice/Oclgrind)
+or [pocl](http://portablecl.org/), e.g. using mamba / conda. Oclgrind is recommended for Windows systems, PoCL for Linux. MacOS typically comes with OpenCL support for CPUs.
+
+```
+mamba install oclgrind -c conda-forge
+```
+
+OR
+
+```
+mamba install pocl -c conda-forge
+```
+
+Owners of compatible Intel Xeon CPUs can also install a driver to use them for computing:
+* [Intel CPU OpenCL drivers](https://www.intel.com/content/www/us/en/developer/articles/tool/opencl-drivers.html#latest_CPU_runtime)
+
+
+## Example code
+A basic image processing workflow loads blobs.gif and counts the number of objects:
+
+```python
+import pyclesperanto_prototype as cle
+
+from skimage.io import imread, imsave
+
+# initialize / select GPU with "TX" in their name
+device = cle.select_device("TX")
+print("Used GPU: ", device)
+
+# load data
+image = imread('https://imagej.nih.gov/ij/images/blobs.gif')
+
+# process the image
+inverted = cle.subtract_image_from_scalar(image, scalar=255)
+blurred = cle.gaussian_blur(inverted, sigma_x=1, sigma_y=1)
+binary = cle.threshold_otsu(blurred)
+labeled = cle.connected_components_labeling_box(binary)
+
+# The maximium intensity in a label image corresponds to the number of objects
+num_labels = labeled.max()
+print(f"Number of objects in the image: {num_labels}")
+
+# save image to disc
+imsave("result.tif", labeled)
+```
+
+## Example gallery
+
+<table border="0">
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_select_GPU.png" width="300"/>
+
+</td><td>
+
+[Select GPU](https://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/select_GPU.py)
+
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/jupyter.png" width="300"/>
+
+</td><td>
+
+[Image processing in Jupyter Notebooks](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/interoperability/jupyter.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_count_blobs.png" width="300"/>
+
+</td><td>
+
+[Counting blobs](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/count_blobs.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/voronoi_otsu_labeling.png" width="300"/>
+
+</td><td>
+
+[Voronoi-Otsu labeling](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/segmentation/voronoi_otsu_labeling.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/segmentation_3d.png" width="300"/>
+
+</td><td>
+
+[3D Image segmentation ](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/segmentation/Segmentation_3D.ipynb)
+
+</td></tr>
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/segmentation_2d_membranes.png" width="300"/>
+
+</td><td>
+
+[Cell segmentation based on membranes](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/segmentation/segmentation_2d_membranes.ipynb)
+
+</td></tr>
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/counting_nuclei_multichannel.png" width="300"/>
+
+</td><td>
+
+[Counting nuclei according to expression in multiple channels](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/measurement/counting_nuclei_multichannel.ipynb)
+
+</td></tr>
+
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/differentiate_nuclei_intensity.png" width="300"/>
+
+</td><td>
+
+[Differentiating nuclei according to signal intensity](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/measurement/differentiate_nuclei_intensity.ipynb)
+
+</td></tr>
+
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/bead_segmentation.png" width="300"/>
+
+</td><td>
+
+[Detecting beads and measuring their size](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/segmentation/bead_segmentation.ipynb)
+
+</td></tr>
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/label_statistics.png" width="300"/>
+
+</td><td>
+
+[Label statistics](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/label_statistics.ipynb)
+
+</td></tr>
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/parametric_maps.png" width="300"/>
+
+</td><td>
+
+[Parametric maps](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/tissues/parametric_maps.ipynb)
+
+</td></tr>
+
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/intensities_along_lines.png" width="300"/>
+
+</td><td>
+
+[Measure intensity along lines](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/measurement/intensities_along_lines.ipynb)
+
+</td></tr>
+
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_crop_and_paste_images.png" width="300"/>
+
+</td><td>
+
+[Crop and paste images](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/crop_and_paste_images.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_inspecting_3d_images.png" width="300"/>
+
+</td><td>
+
+[Inspecting 3D image data](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/inspecting_3d_images.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_affine_transforms.png" width="300"/>
+
+</td><td>
+
+[Rotation, scaling, translation, affine transforms](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/transforms/affine_transforms.ipynb)
+
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_deskew.png" width="300"/>
+
+</td><td>
+
+[Deskewing](https://github.com/clEsperanto/pyclesperanto_prototype/blob/master/demo/transforms/deskew.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_multiply_vectors_and_matrices.png" width="300"/>
+
+</td><td>
+
+[Multiply vectors and matrices](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/multiply_vectors_and_matrices.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_multiply_matrices.png" width="300"/>
+
+</td><td>
+
+[Matrix multiplication](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/multiply_matrices.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_spots_pointlists_matrices_tables.png" width="300"/>
+
+</td><td>
+
+* [Working with spots, pointlist and matrices](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/spots_pointlists_matrices_tables.ipynb)
+* [Lists of nonzero pixel coordinates](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/nonzero.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/mesh_between_centroids.png" width="300"/>
+
+</td><td>
+
+[Mesh between centroids](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/mesh_between_centroids.ipynb)
+
+</td></tr><tr><td>
+
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/mesh_between_touching_neighbors.png" width="300"/>
+
+</td><td>
+
+[Mesh between touching neighbors](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/mesh_between_touching_neighbors.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/mesh_with_distances.png" width="300"/>
+
+</td><td>
+
+[Mesh with distances](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/mesh_with_distances.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/mesh_nearest_neighbors.png" width="300"/>
+
+</td><td>
+
+[Mesh nearest_neighbors](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/mesh_nearest_neighbors.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/ipgraph_networkx.png" width="300"/>
+
+</td><td>
+
+[Export to igraph and networkx](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/ipgraph_networkx.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/neighborhood_definitions.png" width="300"/>
+
+</td><td>
+
+[Neighborhood definitions](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/neighborhood_definitions.ipynb)
+
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/tissue_neighborhood_quantification.png" width="300"/>
+
+</td><td>
+
+[Tissue neighborhood quantification](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/tissues/tissue_neighborhood_quantification.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/neighbors_of_neighbors.png" width="300"/>
+
+</td><td>
+
+[Neighbors of neighbors](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/neighbors_of_neighbors.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_voronoi_diagrams.png" width="300"/>
+
+</td><td>
+
+[Voronoi diagrams](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/voronoi_diagrams.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/shape_descriptors_based_on_neighborhood_graphs.png" width="300"/>
+
+</td><td>
+
+[Shape descriptors based on neighborhood graphs](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/shape_descriptors_based_on_neighborhood_graphs.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/distance_to_other_labels.png" width="300"/>
+
+</td><td>
+
+[Measuring distances between labels in two label images](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/distance_to_other_labels.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_tribolium_napari.png" width="300"/>
+
+</td><td>
+
+[Tribolium morphometry + Napari](https://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/tribolium_morphometry/tribolium.py)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_tribolium_morphometry.png" width="300"/>
+
+</td><td>
+
+[Tribolium morphometry](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/tribolium_morphometry/tribolium_morphometry2.ipynb)
+[(archived version)](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/tribolium_morphometry/tribolium_morphometry.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_napari_dask.png" width="300"/>
+
+</td><td>
+
+[napari+dask timelapse processing](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/napari_gui/napari_dask.ipynb)
+
+</td></tr>
+</table>
+
+## Technical insights
+
+<table border="0"><tr><td>
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/browse_operations.png" width="300"/>
+
+</td><td>
+
+[Browsing operations](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/browse_operations.ipynb)
+
+</td></tr>
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/interactive_widgets.gif" width="300"/>
+
+</td><td>
+
+[Interactive widgets](https://colab.research.google.com/github/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/browse_operations.ipynb)
+
+</td></tr>
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/optimize_blobs_segmentation.png" width="300"/>
+
+</td><td>
+
+[Automatic workflow optimization](https://colab.research.google.com/github/clEsperanto/pyclesperanto_prototype/tree/master/demo/optimization/optimize_blobs_segmentation.ipynb)
+
+</td></tr>
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/memory_management.png" width="300"/>
+
+</td><td>
+
+[Tracing memory consumtion on NVidia GPUs](https://github.com/clEsperanto/pyclesperanto_prototype/blob/master/demo/optimization/memory_management.ipynb)
+
+</td></tr>
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/switching_gpus.png" width="300"/>
+
+</td><td>
+
+[Exploring and switching between GPUs](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/switching_gpus.ipynb)
+
+</td></tr>
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/cupy_compatibility.png" width="300"/>
+
+</td><td>
+
+[Interoperability with cupy](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/interoperability_cupy.ipynb)
+
+[Using the cupy backend](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/select_backend.ipynb)
+
+</td></tr>
+<tr><td>
+
+<img src="./docs/images/dask.jpg" width="300"/>
+
+</td><td>
+
+[Big data handling with Dask GPU clusters](./demo/interoperability/dask.ipynb)
+
+
+</td></tr>
+</table>
+
+## Related projects
+
+<table border="0"><tr><td>
+
+<img src="https://github.com/clesperanto/napari_pyclesperanto_assistant/raw/master/docs/images/screenshot.png" width="300"/>
+
+</td><td>
+
+[napari-pyclesperanto-assistant](https://github.com/clesperanto/napari_pyclesperanto_assistant):
+A graphical user interface for general purpose GPU-accelerated image processing and analysis in napari.
+
+</td></tr><tr><td>
+
+<img src="https://github.com/haesleinhuepf/napari-accelerated-pixel-and-object-classification/raw/main/images/screenshot.png" width="300"/>
+
+</td><td>
+
+[napari-accelerated-pixel-and-object-classification](https://github.com/haesleinhuepf/napari-accelerated-pixel-and-object-classification):
+GPU-accelerated Random Forest Classifiers for pixel and labeled object classification
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/napari-clusters-plotter.png" width="300"/>
+
+</td><td>
+
+[napari-clusters-plotter](https://github.com/BiAPoL/napari-clusters-plotter):
+Clustering of objects according to their quantitative properties
+
+</td></tr></table>
+
+## Benchmarking
+We implemented some basic benchmarking notebooks allowing to see performance differences between pyclesperanto and
+some other image processing libraries, typically using the CPU. Such benchmarking results vary heavily depending on
+image size, kernel size, used operations, parameters and used hardware. Feel free to use those notebooks, adapt them to
+your use-case scenario and benchmark on your target hardware. If you have different scenarios or use-cases, you are very
+welcome to submit your notebook as pull-request!
+
+* [Affine transforms](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/affine_transforms.ipynb)
+* [Background subtraction](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/top_hat.ipynb)
+* [Gaussian blur](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/gaussian_blur.ipynb)
+* [Convolution](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/convolution.ipynb)
+* [Otsu's thresholding](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/threshold_otsu.ipynb)
+* [Connected component labeling](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/connected_component_labeling.ipynb)
+* [Extend labels](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/extend_labels.ipynb)
+* [Statistics of labeled pixels / regionprops](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/statistics_of_labeled_pixels.ipynb)
+* [Histograms](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/histograms.ipynb)
+* [Matrix multiplication](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/matrix_multiplication.ipynb)
+* [Pixel-wise comparison](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/pixelwise_comparison.ipynb)
+* [Intensity projections](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/intensity_projections.ipynb)
+* [Axis transposition](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/transpose.ipynb)
+* [Nonzero](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/nonzero.ipynb)
+
+## See also
+There are other libraries for code acceleration and GPU-acceleration for image processing.
+* [numba](https://numba.pydata.org/)
+* [cupy](https://cupy.dev)
+* [cucim](https://github.com/rapidsai/cucim)
+* [clij](https://clij.github.io)
+
+## Feedback welcome!
+clesperanto is developed in the open because we believe in the open source community. See our [community guidelines](https://clij.github.io/clij2-docs/community_guidelines). Feel free to drop feedback as [github issue](https://github.com/clEsperanto/pyclesperanto_prototype/issues) or via [image.sc](https://image.sc)
+ + +%package help +Summary: Development documents and examples for pyclesperanto-prototype +Provides: python3-pyclesperanto-prototype-doc +%description help +# py-clesperanto
+[](https://forum.image.sc/tag/clesperanto)
+[](http://clesperanto.net)
+[](https://pypi.org/project/pyclesperanto-prototype)
+[](https://anaconda.org/conda-forge/pyclesperanto-prototype)
+[](https://github.com/clEsperanto/pyclesperanto_prototype/graphs/contributors)
+[](https://pypistats.org/packages/pyclesperanto_prototype)
+[](https://github.com/clEsperanto/pyclesperanto_prototype/)
+[](https://github.com/clEsperanto/pyclesperanto_prototype/)
+[](https://github.com/haesleinhuepf/pyclesperanto_prototype/raw/master/LICENSE)
+[](https://python.org)
+[](https://github.com/clesperanto/pyclesperanto_prototype/actions)
+[](https://codecov.io/gh/clesperanto/pyclesperanto_prototype)
+[](https://en.wikipedia.org/wiki/Software_release_life_cycle#Alpha)
+[](https://zenodo.org/badge/latestdoi/248206619)
+
+py-clesperanto is a prototype for [clesperanto](http://clesperanto.net) - a multi-platform multi-language framework for GPU-accelerated image processing.
+We mostly use it in the life sciences for analysing 3- and 4-dimensional microsopy data, e.g. as we face it developmental biology when segmenting cells and studying
+their individual properties as well as properties of compounds of cells forming tissues.
+
+
+Image data source: Daniela Vorkel, Myers lab, MPI-CBG, rendered using [napari](https://github.com/napari/napari)
+
+clesperanto uses [OpenCL kernels](https://github.com/clEsperanto/clij-opencl-kernels/tree/development/src/main/java/net/haesleinhuepf/clij/kernels) from [CLIJ](http://clij.github.io/).
+
+For users convenience, there are code generators available for [napari](https://clesperanto.github.io/napari_pyclesperanto_assistant/) and [Fiji](https://clij.github.io/assistant/).
+Also check out the [napari workflow optimizer](https://github.com/haesleinhuepf/napari-workflow-optimizer) for semi-automatic parameter tuning of clesperanto-functions.
+
+## Reference
+The preliminary API reference is available [here](https://clesperanto.github.io/pyclesperanto_prototype/docs/_build/html/).
+Furthermore, parts of the [reference](https://clij.github.io/clij2-docs/reference__pyclesperanto) are also available within the CLIJ2 documentation.
+
+## Installation
+* Get a conda/python environment, e.g. via [mamba-forge](https://github.com/conda-forge/miniforge#mambaforge).
+* If you never used python/conda environments before, please follow [these instructions](https://biapol.github.io/blog/mara_lampert/getting_started_with_mambaforge_and_python/readme.html) first.
+
+```
+conda create --name cle_39 python=3.9
+conda activate cle_39
+```
+
+* Install pyclesperanto-prototype using [mamba / conda](https://focalplane.biologists.com/2022/12/08/managing-scientific-python-environments-using-conda-mamba-and-friends/):
+
+```
+mamba install -c conda-forge pyclesperanto-prototype
+```
+
+OR using pip:
+
+```
+pip install pyclesperanto-prototype
+```
+
+## Troubleshooting: Graphics cards drivers
+
+In case error messages contains "ImportError: DLL load failed while importing cl: The specified procedure could not be found" [see also](https://github.com/clEsperanto/pyclesperanto_prototype/issues/55) or "clGetPlatformIDs failed: PLATFORM_NOT_FOUND_KHR", please install recent drivers for your graphics card and/or OpenCL device. Select the right driver source depending on your hardware from this list:
+
+* [AMD drivers](https://www.amd.com/en/support)
+* [NVidia drivers](https://www.nvidia.com/download/index.aspx)
+* [Intel GPU drivers](https://www.intel.com/content/www/us/en/download/726609/intel-arc-graphics-windows-dch-driver.html)
+* [Microsoft Windows OpenCL support](https://www.microsoft.com/en-us/p/opencl-and-opengl-compatibility-pack/9nqpsl29bfff)
+
+Sometimes, mac-users need to install this:
+
+ mamba install -c conda-forge ocl_icd_wrapper_apple
+
+Sometimes, linux users need to install this:
+
+ mamba install -c conda-forge ocl-icd-system
+
+## Computing on Central Processing units (CPUs)
+
+If no OpenCL-compatible GPU is available, pyclesperanto-prototype can make use of CPUs instead.
+Just install [oclgrind](https://github.com/jrprice/Oclgrind)
+or [pocl](http://portablecl.org/), e.g. using mamba / conda. Oclgrind is recommended for Windows systems, PoCL for Linux. MacOS typically comes with OpenCL support for CPUs.
+
+```
+mamba install oclgrind -c conda-forge
+```
+
+OR
+
+```
+mamba install pocl -c conda-forge
+```
+
+Owners of compatible Intel Xeon CPUs can also install a driver to use them for computing:
+* [Intel CPU OpenCL drivers](https://www.intel.com/content/www/us/en/developer/articles/tool/opencl-drivers.html#latest_CPU_runtime)
+
+
+## Example code
+A basic image processing workflow loads blobs.gif and counts the number of objects:
+
+```python
+import pyclesperanto_prototype as cle
+
+from skimage.io import imread, imsave
+
+# initialize / select GPU with "TX" in their name
+device = cle.select_device("TX")
+print("Used GPU: ", device)
+
+# load data
+image = imread('https://imagej.nih.gov/ij/images/blobs.gif')
+
+# process the image
+inverted = cle.subtract_image_from_scalar(image, scalar=255)
+blurred = cle.gaussian_blur(inverted, sigma_x=1, sigma_y=1)
+binary = cle.threshold_otsu(blurred)
+labeled = cle.connected_components_labeling_box(binary)
+
+# The maximium intensity in a label image corresponds to the number of objects
+num_labels = labeled.max()
+print(f"Number of objects in the image: {num_labels}")
+
+# save image to disc
+imsave("result.tif", labeled)
+```
+
+## Example gallery
+
+<table border="0">
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_select_GPU.png" width="300"/>
+
+</td><td>
+
+[Select GPU](https://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/select_GPU.py)
+
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/jupyter.png" width="300"/>
+
+</td><td>
+
+[Image processing in Jupyter Notebooks](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/interoperability/jupyter.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_count_blobs.png" width="300"/>
+
+</td><td>
+
+[Counting blobs](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/count_blobs.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/voronoi_otsu_labeling.png" width="300"/>
+
+</td><td>
+
+[Voronoi-Otsu labeling](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/segmentation/voronoi_otsu_labeling.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/segmentation_3d.png" width="300"/>
+
+</td><td>
+
+[3D Image segmentation ](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/segmentation/Segmentation_3D.ipynb)
+
+</td></tr>
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/segmentation_2d_membranes.png" width="300"/>
+
+</td><td>
+
+[Cell segmentation based on membranes](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/segmentation/segmentation_2d_membranes.ipynb)
+
+</td></tr>
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/counting_nuclei_multichannel.png" width="300"/>
+
+</td><td>
+
+[Counting nuclei according to expression in multiple channels](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/measurement/counting_nuclei_multichannel.ipynb)
+
+</td></tr>
+
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/differentiate_nuclei_intensity.png" width="300"/>
+
+</td><td>
+
+[Differentiating nuclei according to signal intensity](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/measurement/differentiate_nuclei_intensity.ipynb)
+
+</td></tr>
+
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/bead_segmentation.png" width="300"/>
+
+</td><td>
+
+[Detecting beads and measuring their size](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/segmentation/bead_segmentation.ipynb)
+
+</td></tr>
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/label_statistics.png" width="300"/>
+
+</td><td>
+
+[Label statistics](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/label_statistics.ipynb)
+
+</td></tr>
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/parametric_maps.png" width="300"/>
+
+</td><td>
+
+[Parametric maps](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/tissues/parametric_maps.ipynb)
+
+</td></tr>
+
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/intensities_along_lines.png" width="300"/>
+
+</td><td>
+
+[Measure intensity along lines](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/measurement/intensities_along_lines.ipynb)
+
+</td></tr>
+
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_crop_and_paste_images.png" width="300"/>
+
+</td><td>
+
+[Crop and paste images](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/crop_and_paste_images.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_inspecting_3d_images.png" width="300"/>
+
+</td><td>
+
+[Inspecting 3D image data](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/inspecting_3d_images.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_affine_transforms.png" width="300"/>
+
+</td><td>
+
+[Rotation, scaling, translation, affine transforms](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/transforms/affine_transforms.ipynb)
+
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_deskew.png" width="300"/>
+
+</td><td>
+
+[Deskewing](https://github.com/clEsperanto/pyclesperanto_prototype/blob/master/demo/transforms/deskew.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_multiply_vectors_and_matrices.png" width="300"/>
+
+</td><td>
+
+[Multiply vectors and matrices](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/multiply_vectors_and_matrices.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_multiply_matrices.png" width="300"/>
+
+</td><td>
+
+[Matrix multiplication](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/multiply_matrices.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_spots_pointlists_matrices_tables.png" width="300"/>
+
+</td><td>
+
+* [Working with spots, pointlist and matrices](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/spots_pointlists_matrices_tables.ipynb)
+* [Lists of nonzero pixel coordinates](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/nonzero.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/mesh_between_centroids.png" width="300"/>
+
+</td><td>
+
+[Mesh between centroids](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/mesh_between_centroids.ipynb)
+
+</td></tr><tr><td>
+
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/mesh_between_touching_neighbors.png" width="300"/>
+
+</td><td>
+
+[Mesh between touching neighbors](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/mesh_between_touching_neighbors.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/mesh_with_distances.png" width="300"/>
+
+</td><td>
+
+[Mesh with distances](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/mesh_with_distances.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/mesh_nearest_neighbors.png" width="300"/>
+
+</td><td>
+
+[Mesh nearest_neighbors](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/mesh_nearest_neighbors.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/ipgraph_networkx.png" width="300"/>
+
+</td><td>
+
+[Export to igraph and networkx](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/ipgraph_networkx.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/neighborhood_definitions.png" width="300"/>
+
+</td><td>
+
+[Neighborhood definitions](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/neighborhood_definitions.ipynb)
+
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/tissue_neighborhood_quantification.png" width="300"/>
+
+</td><td>
+
+[Tissue neighborhood quantification](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/tissues/tissue_neighborhood_quantification.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/neighbors_of_neighbors.png" width="300"/>
+
+</td><td>
+
+[Neighbors of neighbors](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/neighbors_of_neighbors.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_voronoi_diagrams.png" width="300"/>
+
+</td><td>
+
+[Voronoi diagrams](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/voronoi_diagrams.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/shape_descriptors_based_on_neighborhood_graphs.png" width="300"/>
+
+</td><td>
+
+[Shape descriptors based on neighborhood graphs](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/shape_descriptors_based_on_neighborhood_graphs.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/distance_to_other_labels.png" width="300"/>
+
+</td><td>
+
+[Measuring distances between labels in two label images](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/neighbors/distance_to_other_labels.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_tribolium_napari.png" width="300"/>
+
+</td><td>
+
+[Tribolium morphometry + Napari](https://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/tribolium_morphometry/tribolium.py)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_tribolium_morphometry.png" width="300"/>
+
+</td><td>
+
+[Tribolium morphometry](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/tribolium_morphometry/tribolium_morphometry2.ipynb)
+[(archived version)](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/tribolium_morphometry/tribolium_morphometry.ipynb)
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_napari_dask.png" width="300"/>
+
+</td><td>
+
+[napari+dask timelapse processing](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/napari_gui/napari_dask.ipynb)
+
+</td></tr>
+</table>
+
+## Technical insights
+
+<table border="0"><tr><td>
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/browse_operations.png" width="300"/>
+
+</td><td>
+
+[Browsing operations](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/browse_operations.ipynb)
+
+</td></tr>
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/interactive_widgets.gif" width="300"/>
+
+</td><td>
+
+[Interactive widgets](https://colab.research.google.com/github/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/browse_operations.ipynb)
+
+</td></tr>
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/optimize_blobs_segmentation.png" width="300"/>
+
+</td><td>
+
+[Automatic workflow optimization](https://colab.research.google.com/github/clEsperanto/pyclesperanto_prototype/tree/master/demo/optimization/optimize_blobs_segmentation.ipynb)
+
+</td></tr>
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/memory_management.png" width="300"/>
+
+</td><td>
+
+[Tracing memory consumtion on NVidia GPUs](https://github.com/clEsperanto/pyclesperanto_prototype/blob/master/demo/optimization/memory_management.ipynb)
+
+</td></tr>
+
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/switching_gpus.png" width="300"/>
+
+</td><td>
+
+[Exploring and switching between GPUs](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/switching_gpus.ipynb)
+
+</td></tr>
+<tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/cupy_compatibility.png" width="300"/>
+
+</td><td>
+
+[Interoperability with cupy](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/interoperability_cupy.ipynb)
+
+[Using the cupy backend](http://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/basics/select_backend.ipynb)
+
+</td></tr>
+<tr><td>
+
+<img src="./docs/images/dask.jpg" width="300"/>
+
+</td><td>
+
+[Big data handling with Dask GPU clusters](./demo/interoperability/dask.ipynb)
+
+
+</td></tr>
+</table>
+
+## Related projects
+
+<table border="0"><tr><td>
+
+<img src="https://github.com/clesperanto/napari_pyclesperanto_assistant/raw/master/docs/images/screenshot.png" width="300"/>
+
+</td><td>
+
+[napari-pyclesperanto-assistant](https://github.com/clesperanto/napari_pyclesperanto_assistant):
+A graphical user interface for general purpose GPU-accelerated image processing and analysis in napari.
+
+</td></tr><tr><td>
+
+<img src="https://github.com/haesleinhuepf/napari-accelerated-pixel-and-object-classification/raw/main/images/screenshot.png" width="300"/>
+
+</td><td>
+
+[napari-accelerated-pixel-and-object-classification](https://github.com/haesleinhuepf/napari-accelerated-pixel-and-object-classification):
+GPU-accelerated Random Forest Classifiers for pixel and labeled object classification
+
+</td></tr><tr><td>
+
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/napari-clusters-plotter.png" width="300"/>
+
+</td><td>
+
+[napari-clusters-plotter](https://github.com/BiAPoL/napari-clusters-plotter):
+Clustering of objects according to their quantitative properties
+
+</td></tr></table>
+
+## Benchmarking
+We implemented some basic benchmarking notebooks allowing to see performance differences between pyclesperanto and
+some other image processing libraries, typically using the CPU. Such benchmarking results vary heavily depending on
+image size, kernel size, used operations, parameters and used hardware. Feel free to use those notebooks, adapt them to
+your use-case scenario and benchmark on your target hardware. If you have different scenarios or use-cases, you are very
+welcome to submit your notebook as pull-request!
+
+* [Affine transforms](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/affine_transforms.ipynb)
+* [Background subtraction](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/top_hat.ipynb)
+* [Gaussian blur](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/gaussian_blur.ipynb)
+* [Convolution](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/convolution.ipynb)
+* [Otsu's thresholding](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/threshold_otsu.ipynb)
+* [Connected component labeling](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/connected_component_labeling.ipynb)
+* [Extend labels](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/extend_labels.ipynb)
+* [Statistics of labeled pixels / regionprops](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/statistics_of_labeled_pixels.ipynb)
+* [Histograms](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/histograms.ipynb)
+* [Matrix multiplication](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/matrix_multiplication.ipynb)
+* [Pixel-wise comparison](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/pixelwise_comparison.ipynb)
+* [Intensity projections](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/intensity_projections.ipynb)
+* [Axis transposition](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/transpose.ipynb)
+* [Nonzero](http://github.com/clEsperanto/pyclesperanto_prototype/blob/master/benchmarks/nonzero.ipynb)
+
+## See also
+There are other libraries for code acceleration and GPU-acceleration for image processing.
+* [numba](https://numba.pydata.org/)
+* [cupy](https://cupy.dev)
+* [cucim](https://github.com/rapidsai/cucim)
+* [clij](https://clij.github.io)
+
+## Feedback welcome!
+clesperanto is developed in the open because we believe in the open source community. See our [community guidelines](https://clij.github.io/clij2-docs/community_guidelines). Feel free to drop feedback as [github issue](https://github.com/clEsperanto/pyclesperanto_prototype/issues) or via [image.sc](https://image.sc)
+ + +%prep +%autosetup -n pyclesperanto-prototype-0.24.1 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-pyclesperanto-prototype -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Wed May 10 2023 Python_Bot <Python_Bot@openeuler.org> - 0.24.1-1 +- Package Spec generated @@ -0,0 +1 @@ +2b55c47e978ccf4f7bc5e50b5a38befa pyclesperanto_prototype-0.24.1.tar.gz |