python-microscopy

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The python-microscopy environment - an open-source package for light microscopy

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- - bug_report.md
  - feature_request.md
  - proposal.md
  - support.md
- - build_docs.yml
  - build_pip.yml
  - codeql-analysis.yml
  - lint.yml
  - make_installers.yaml
  - make_release.yml
  - pr_check.yml
  - test_report.yml
- PULL_REQUEST_TEMPLATE.md
- - _run_test.py
  - bld.bat
  - build.sh
  - conda_build_config.yaml
  - entry_points.yaml
  - menu-windows.json
  - meta.yaml
  - pymeLogo.png
- - theme_overrides.css
- - layout.html
- - modules.rst
  - PYME.rst
- - cluster_compute.rst
  - cluster_install.rst
  - clusterFilesystem.rst
  - PYMECluster.rst
- - executable_installers.md
  - README.md
- - distancecolocalization.rst
- - anaconda_nav_add_chan_update.png
  - anaconda_nav_add_channel.png
  - anaconda_nav_add_channel_david_baddeley.png
  - anaconda_nav_install_python-microscopy.png
  - anaconda_navigator.png
  - correlation_drift_dialog.png
  - dh5view_lm.png
  - disp_panel.png
  - drift_colour_coded.png
  - drift_est_corr_graph.png
  - drift_est_corr_graph_2.png
  - drift_plot.png
  - extracted_psf.png
  - extracted_PSF_CRLB.png
  - filter_edit.png
  - filter_edit.xcf
  - filter_panel.png
  - filter_panel.xcf
  - generate_triangulation_dialog.png
  - generated_image.png
  - import_mat.png
  - Import_text_dialog.png
  - interactive_display.png
  - overlay_and_panel.png
  - pipeline_new.png
  - psf_extraction_gui.png
  - psf_extraction_tagged.png
  - pyme_acquire_ui.png
  - recipe.png
  - SampleDB_schem_no_tags.png
  - tagged_psfs_xz.png
  - traits_generated_gui.png
  - view_modes.png
  - vis_gui_data_loaded.png
  - vis_gui_data_loaded.xcf
  - vis_pipeline.pdf
  - vis_pipeline.svg
  - VisGUI_FileOpen.png
  - VisGUI_NoData.png
- - Installation.rst
  - InstallationFromSource.rst
  - InstallationWithAnaconda.rst
  - InstallationWithAnacondaNoConsole.rst
- - animation.rst
  - appendix.rst
  - data_correction.rst
  - data_exploration.rst
  - edit_recipe.rst
  - image_reconstruction.rst
  - programmatic_usage.rst
  - quantification.rst
  - segmentation.rst
  - surface_extraction.rst
  - synthetic_data.rst
- AcquireBasicUsage.rst
- AnalysingForeignData.rst
- Analysis.rst
- apidoc.py
- BasicAcquisition.rst
- component_programs.rst
- conf.py
- ConfiguringPYMEAcquire.rst
- Contributing.rst
- DataFormats.rst
- DataModel.rst
- dh5view.rst
- ExtendingDsviewer.rst
- ExtendingVisGUI.rst
- gen_api_docs
- hacking.rst
- index.rst
- LocalisationAnalysis.rst
- make.bat
- Makefile
- metadata.rst
- ModifyingPYMEAcquire.rst
- Protocols.rst
- PSFExtraction.rst
- PYMEAcquire.rst
- PYMEImage_rendering.rst
- PYMEVis.rst
- Recipes.rst
- SampleDB.rst
- Simulator.rst
- SplitterMulticolour.rst
- supported_hardware.rst
- Technical.rst
- tiff_handling.rst
- VisGUI.rst
- WritingRecipeModules.rst
- - pyme_setup.iss
- install-python-microscopy.bat
- install-python-microscopy.sh
- INSTALLERS.md
- - __init__.py
  - auto_drift_render.py
  - auto_photophysics.py
- calenderApi.py
- multicolourMeta.py
- README.md
- shellutils.py
- startCommentify.py
- twoColDep.py
- - AppDelegate.h
  - AppDelegate.m
  - Info.plist
  - main.m
- - project.pbxproj
- - AppDelegate.h
  - AppDelegate.m
  - Info.plist
  - main.m
- text5377.png
- - __init__.py
  - acquire_app.py
  - acquire_client.py
  - acquire_server.py
  - acquirebase.py
  - acquiremainframe.py
  - acquirewx.py
  - acquisition_base.py
  - ActionManager.py
  - actions.py
  - autofocus.py
  - event_loop.py
  - eventLog.py
  - ExecTools.py
  - frameWrangler.py
  - logging.yaml
  - meson.build
  - microscope.py
  - positionTracker.py
  - protocol.py
  - protocol_acquisition.py
  - PYMEAcquire.py
  - sampleInformation.py
  - sampleInformationDjangoDirect.py
  - setup.py
  - SpoolController.py
  - stackSettings.py
  - stage_leveling.py
  - xyztc.py
  - zScanner.py
- - __init__.py
  - _fithelpers.py
  - angleFilter.py
  - annealThresh.py
  - autoencoder_classifier.py
  - binAvg.py
  - composite.py
  - cramerRao.py
  - density_filter.py
  - deTile.py
  - distributed_pyramid.py
  - fiducial_matching.py
  - gen_sCMOS_maps.py
  - graphing_filters.py
  - implicitFilter.py
  - keep_pairs.py
  - meson.build
  - MetaData.py
  - optic_flow.py
  - piecewise.py
  - piecewiseMapping.py
  - piezo_movement_correction.py
  - processLogger.py
  - profile_extraction.py
  - setup.py
  - splitting.py
  - svmSegment.py
  - thresholding.py
  - tile_pyramid.py
  - widefieldify.py
- - __init__.py
  - cluster_of_one.py
  - dataserver_wsgi.py
  - distribution.py
  - HTTPDataServer.py
  - HTTPRulePusher.py
  - HTTPTaskPusher.py
  - PYMERuleNodeServer.py
  - PYMERuleServer.py
  - rulenodeserver.py
  - rules.py
  - ruleserver.py
  - status.py
  - taskWorkerHTTP.py
  - webdav.py
- - __init__.py
  - auiFloatBook.py
  - congrid.py
  - listctrlMixins.py
  - lzw.py
  - meson.build
  - setup.py
  - TextCtrlAutoComplete.py
  - wxPlotPanel.py
- - __init__.py
  - beadGen.py
  - dec.py
  - dec_test.py
  - deconvDialogs.py
  - decTask.py
  - decThread.py
  - fftwWisdom.py
  - gen_2ph_4piA_psf.m
  - richardsonLucy.py
  - richardsonLucyMV.py
  - richardsonLucyMVM.py
  - test_block_dec.py
  - tq_block_dec.py
  - wiener.py
- - __init__.py
  - arrayViewPanel.py
  - displayOptions.py
  - DisplayOptionsPanel.py
  - displaySettingsPanel.py
  - dsviewer.py
  - eventLogViewer.py
  - fitInfo.py
  - htmlServe.py
  - logparser.py
  - meson.build
  - OpenSequenceDialog.py
  - overlays.py
  - OverlaysPanel.py
  - PYMEImage.py
  - scrolledImagePanel.py
  - setup.py
  - splashScreen.py
  - voxSizeDialog.py
- - __init__.pxd
  - __init__.py
  - _octree.pyx
  - _treap.pyx
  - _triangle_mesh.pxd
  - _triangle_mesh.pyx
  - aqavg.py
  - dcimg_chuck_test.py
  - dcimgFileChucker.py
  - dcimgSpoolShim.py
  - dual_marching_cubes.py
  - dual_marching_cubes_v2.py
  - expectationMaximisation.py
  - func_octree.pyx
  - func_octree.pyx.c
  - fusionRadial.py
  - fusionUtils.py
  - isosurface.py
  - labview_spooling_hacks.py
  - marching_cubes.py
  - marching_tetrahedra.py
  - meson.build
  - modified_marching_cubes.py
  - music.py
  - octree.py
  - pointFitConfoc.py
  - pSpaceMap.py
  - remesh_ops.c
  - remesh_ops.h
  - scanner_control.py
  - setup.py
  - SimReconstruction.py
  - spark.py
  - tcHist.py
  - treap.py
  - triangle_mesh.py
  - triangle_mesh_utils.c
  - triangle_mesh_utils.h
  - triangle_utils.py
  - triangular_mesh.py
  - zMotionArtifactUtils.py
- - __init__.py
  - acquisition_backends.py
  - buffer_helpers.pyx
  - buffers.py
  - cluster_directory.py
  - cluster_streaming.py
  - clusterDuplication.py
  - clusterExport.py
  - clusterGlob.py
  - clusterIO.py
  - clusterListing.py
  - clusterResults.py
  - clusterUpload.py
  - compatibility.py
  - csv_flavours.py
  - dataExporter.py
  - dataWrap.py
  - dcimg.py
  - events.py
  - h5File.py
  - h5rFile.py
  - HTTPSpooler_v2.py
  - image.py
  - load_psf.py
  - meson.build
  - MetaDataHandler.py
  - pyme_h5ls.py
  - PZFFormat.py
  - ragged.py
  - rgb_image.py
  - setup.py
  - Spooler.py
  - tabular.py
  - testClusterSpooling.py
  - unifiedIO.py
  - zarr_compat.py
- - __init__.py
  - colourFilterGUI.py
  - colourPanel.py
  - displayPane.py
  - dyeRatios.py
  - genImageDialog.py
  - gl_offScreenHandler.py
  - gl_render.py
  - gl_render3D.py
  - gl_render3D_shaders.py
  - glcanvas_core.py
  - imageView.py
  - imageView2.py
  - importTextDialog.py
  - layer_panel.py
  - meson.build
  - mv_math.py
  - objectDarkMeasure.py
  - pipeline.py
  - pipelineView.py
  - pointSettingsPanel.py
  - progGraph.py
  - PYMEVisualise.py
  - quadTreeSettings.py
  - renderers.py
  - rendGauss.py
  - sessionpaths.py
  - setup.py
  - setup_exe.py
  - statusLog.py
  - triBlobs.py
  - view_clipping_pane.py
  - views.py
  - visCore.py
  - VisGUI.py
  - visHelpers.py
  - visHelpersMin.py
  - workspaceTree.py
- - __init__.py
  - meson.build
  - MetaDataEdit.py
  - ofind.py
  - ofind3d.py
  - ofind_nofilt.py
  - ofind_pri.py
  - ofind_split.py
  - ofind_xcorr.py
  - ofind_xcorr_fw.py
  - remFitBuf.py
  - setup.py
  - splitting.py
  - twist.py
- - __init__.py
  - aligned_array.py
  - aniso.py
  - big_sur_fix.py
  - check_for_updates.py
  - colormaps.py
  - colorsys.py
  - computerName.py
  - coverslipGeometries.py
  - cython_numpy_monkey.py
  - depGraph.py
  - dirSize.py
  - diskCleanup.py
  - django_widgets.py
  - djangoRecarray.py
  - editgrid.py
  - eventSpy.py
  - exceptions.py
  - facsPlot.py
  - fbpIcons.py
  - fftw_compat.py
  - findCycles.py
  - fortran_interrupt_defeat.py
  - glassModel.py
  - hash32.py
  - hillcurve.py
  - hybrid_ns.py
  - kdFit.py
  - locate.py
  - memmap.py
  - memUsage.py
  - mock_ctypes.py
  - mock_traits.py
  - mock_traitsui.py
  - pyme_zeroconf.py
  - pyro_tracebacks.py
  - read_agf.py
  - sffake.py
  - snells.py
  - sqlite_ns.py
  - sqlitendarray.py
  - taskDef.py
  - tempDB.py
  - TiffImagePlugin.py
  - TiSettings.py
  - VolProj.py
  - wxThread.py
  - zemax.py
  - zernike.py
- - __init__.py
  - DSTaskQueue.py
  - fitMon.py
  - fitMonP.py
  - HDFTaskQueue.py
  - launchWorkers.py
  - setup_exe.py
  - taskQueue.py
  - taskServerZC.py
  - taskWorkerZC.py
- - __init__.py
  - acquisition.py
  - bakeshop.py
  - bakeshop_app.py
  - base.py
  - batchProcess.py
  - filters.py
  - fudges.py
  - graphing.py
  - html_recipe_editor.py
  - localisations.py
  - machine_learning.py
  - measurement.py
  - meson.build
  - modules.py
  - multiview.py
  - output.py
  - pointcloud.py
  - processing.py
  - pyramid.py
  - recipe.py
  - recipe_editor.html
  - recipeGui.py
  - recipeLayout.py
  - runRecipe.py
  - setup.py
  - simulation.py
  - skfilters.py
  - surface_fitting.py
  - tablefilters.py
  - tracking.py
  - traits.py
  - vertical_recipe_display.py
- - __init__.py
  - filters.py
- - __init__.py
  - meson.build
  - setup.py
- - dh5view.cmd
  - dh5view.py
  - fitMonP.py
  - h5-thumbnailer.py
  - h5r-thumbnailer.py
  - launchWorkers.cmd
  - launchWorkers.py
  - lmview.cmd
  - pyme_ascociations.bat
  - pyme_win_postinstall.py
  - PYMEAcquire.cmd
  - PYMEAcquire.py
  - pymeUrlOpener.cmd
  - remove_old_wx.py
  - sf-thumbnailer.py
  - taskServerMP.py
  - taskServerZC.py
  - taskWorkerMP.py
  - taskWorkerZC.py
  - urlOpener.py
  - view3d.py
  - VisGUI.cmd
  - VisGUI.py
  - win_reg.py
- - __init__.py
  - locify.py
  - pointsets.py
  - wormlike.py
  - wormlike2.py
  - wormlike3.py
  - wormlike_curled.py
- - __init__.py
  - tileviewer.py
- - __init__.py
  - about_dlg.py
  - AUIFrame.py
  - autoFoldPanel.py
  - cascading_layout.py
  - crop_dialog.py
  - custom_traits_editors.py
  - editFilterDialog.py
  - editList.py
  - fastGraph.py
  - filterPane.py
  - histLimits.py
  - layerFoldPanel.py
  - manualFoldPanel.py
  - MetadataTree.py
  - mytimer.py
  - patch_traitsui.py
  - progress.py
  - recArrayView.py
  - selection.py
  - shell.py
  - traitsui_constants.py
  - wx_compat.py
- - __init__.py
  - authenticate.py
  - execfile.py
  - install_dependencies.py
  - log_verbosity.py
  - make_installer.bat
  - packageutils.py
  - pymelauncher.py
  - recommended-modules.txt
  - required-modules.txt
  - uilaunch.py
  - webframework.py
- __init__.pxd
- __init__.py
- config.py
- meson.build
- pyme_warnings.py
- setup.py
- setup_exe.py
- UNIT_TEST_README
- update_version.py
- version.py
- - pyme.scss
- make-css.sh
- README.md
- - test_imports.py
.gitignore
ACQUIRE_DEPS.txt
AGENTS.local.md.example
AGENTS.md
BUILD.md
CHANGELOG.md
CLAUDE.md
CODE_OF_CONDUCT.md
codecov.yml
construct.yaml
COPYING
CREDITS
LICENSE
meson.build
post-install-fixscripts.sh
pyproject.toml
README.md
requirements.txt
roadmap.rst
setup.cfg
setup.py
setup_to_meson.py
test_requirements.txt
tox.toml

# Installation Guide

1. Get the code

git clone https://github.com/python-microscopy/python-microscopy

Downloads the entire project code from GitHub to your computer.

cd python-microscopy

Moves into the project folder you just downloaded.

2. CMake

Medium Recommended

Prerequisites

Git Needed to download the project code from GitHub.
CMake The tool used to generate build configuration.
C/C++ 컴파일러 Windows needs Visual Studio (Community edition, free), macOS needs Xcode Command Line Tools, Linux needs the gcc/g++ package.

⚠️ This is a large repository, so this method may point to an internal sub-package rather than the actual core product. Check the full README as well.

cd PYME/Analysis/points/SoftRend/qhull

This project's files live in a subfolder, so move into it first.

mkdir build && cd build

Creates a folder to hold the build output and moves into it.

cmake ..

Analyzes the source code and generates build configuration files (must be run inside the build folder).

make

Compiles the code based on the generated build configuration to produce an executable.

✅ Check that an executable was created inside the build folder, then run it directly (e.g. ./build/app_name).

3. Python

Easy

Prerequisites

Git Needed to download the project code from GitHub.
Python 3 On Windows, be sure to check 'Add Python to PATH' during installation.

⚠️ This is a large repository, so this method may point to an internal sub-package rather than the actual core product. Check the full README as well.

pip install .

Installs the package published on PyPI directly — no need to clone the source.

jupyter notebook

Launches Jupyter in your browser so you can open and run the notebook (.ipynb) files.

✅ If it runs without errors and prints output in the terminal, it worked.

4. Make

Medium

Prerequisites

Git Needed to download the project code from GitHub.
Make Usually pre-installed on Linux/macOS. On Windows, install separately (e.g. via MSYS2 or WSL).

⚠️ This is a large repository, so this method may point to an internal sub-package rather than the actual core product. Check the full README as well.

cd PYME/Analysis/points/SoftRend/qhull

This project's files live in a subfolder, so move into it first.

make

Compiles the code based on the generated build configuration to produce an executable.

✅ If it finishes without errors, it worked. Try running the generated executable directly.

// repository documentation

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