├── Installation and Dependencies.pdf ├── LICENSE ├── README.md ├── Tutorial 0 - Python 101 ├── EM │ ├── EM.py │ ├── __init__.py │ ├── functions.py │ ├── readwrite.py │ └── registration.py ├── EM_forWin │ ├── EM.py │ ├── __init__.py │ ├── functions.py │ ├── readwrite.py │ └── registration.py ├── PARADIM_STEM-summer-school_T0_VM-instructions.pdf ├── PARADIM_STEM-summer-school_T0_notebook-instructions.pdf ├── Tutorial0a-1.ipynb ├── Tutorial0a-2.ipynb ├── Tutorial0a-3.ipynb ├── Tutorial0b.ipynb ├── Verdana.ttf └── images_fornotebook │ ├── FrontendKernel.png │ ├── animation.m4v │ ├── command_mode.png │ ├── dashboard_files_tab.png │ ├── dashboard_files_tab_btns.png │ ├── dashboard_files_tab_new.png │ ├── dashboard_files_tab_run.png │ ├── dashboard_running_tab.png │ ├── edit_mode.png │ ├── ipython_logo.png │ ├── jupyter_logo.png │ ├── menubar_toolbar.png │ ├── nbconvert_arch.png │ └── python_logo.svg ├── Tutorial 1 - STEM Imaging ├── PARADIM_STEM-summer-school_T1_STEM_probe_and_imaging_instructions.pdf ├── Tutorial1_STEM_probe_aberrations.ipynb ├── source │ ├── ctemh.py │ ├── gui.py │ ├── gui_old.py │ ├── incostem.py │ └── stemh.py └── unaberrated.PNG ├── Tutorial 2 - Data Navigation ├── PlugIns │ ├── experimental.zip │ ├── experimental │ │ ├── .github │ │ │ └── workflows │ │ │ │ └── python-package.yml │ │ ├── CHANGES.rst │ │ ├── LICENSE │ │ ├── README.rst │ │ ├── build │ │ │ └── lib │ │ │ │ └── nionswift_plugin │ │ │ │ ├── nion_experimental_4dtools │ │ │ │ ├── CenterOfMass4D.py │ │ │ │ ├── ComputationUI.py │ │ │ │ ├── DarkCorrection4D.py │ │ │ │ ├── DataCache.py │ │ │ │ ├── FramewiseDarkCorrection.py │ │ │ │ ├── ImageChooser.py │ │ │ │ ├── Map4D.py │ │ │ │ ├── Map4DRGB.py │ │ │ │ └── __init__.py │ │ │ │ └── nion_experimental_tools │ │ │ │ ├── AffineTransformImage.py │ │ │ │ ├── AlignMultiSI.py │ │ │ │ ├── AlignSequenceOfMultiDimensionalData.py │ │ │ │ ├── DoubleGaussian.py │ │ │ │ ├── GraphicsTools.py │ │ │ │ ├── MakeColorCOM.py │ │ │ │ ├── MakeIDPC.py │ │ │ │ ├── MeasureZLP.py │ │ │ │ ├── MultiDimensionalProcessing.py │ │ │ │ ├── SequenceSplitJoin.py │ │ │ │ └── __init__.py │ │ ├── dist │ │ │ └── nionswift_experimental-0.7.1-py3.8.egg │ │ ├── meta.yaml │ │ ├── nionswift_experimental.egg-info │ │ │ ├── PKG-INFO │ │ │ ├── SOURCES.txt │ │ │ ├── dependency_links.txt │ │ │ ├── requires.txt │ │ │ └── top_level.txt │ │ ├── nionswift_plugin │ │ │ ├── nion_experimental_4dtools │ │ │ │ ├── 4d_dark_correction.png │ │ │ │ ├── CenterOfMass4D.py │ │ │ │ ├── ComputationUI.py │ │ │ │ ├── DarkCorrection4D.py │ │ │ │ ├── DataCache.py │ │ │ │ ├── FramewiseDarkCorrection.py │ │ │ │ ├── ImageChooser.py │ │ │ │ ├── Map4D.py │ │ │ │ ├── Map4DRGB.py │ │ │ │ ├── README.md │ │ │ │ ├── __init__.py │ │ │ │ └── framewise_dark_correction.png │ │ │ └── nion_experimental_tools │ │ │ │ ├── AffineTransformImage.py │ │ │ │ ├── AlignMultiSI.py │ │ │ │ ├── AlignSequenceOfMultiDimensionalData.py │ │ │ │ ├── DoubleGaussian.py │ │ │ │ ├── GraphicsTools.py │ │ │ │ ├── MakeColorCOM.py │ │ │ │ ├── MakeIDPC.py │ │ │ │ ├── MeasureZLP.py │ │ │ │ ├── MultiDimensionalProcessing.py │ │ │ │ ├── SequenceSplitJoin.py │ │ │ │ ├── __init__.py │ │ │ │ └── test │ │ │ │ ├── AffineTransformImage_test.py │ │ │ │ ├── MultiDimensionalProcessing_test.py │ │ │ │ └── __init__.py │ │ ├── pyproject.toml │ │ ├── scripts │ │ │ ├── AlignZLP.py │ │ │ ├── CompositeSurveyImage.py │ │ │ ├── FindInterface.py │ │ │ ├── MeasureZLPStability.py │ │ │ └── MultiEELS.py │ │ ├── setup.cfg │ │ ├── setup.py │ │ └── test-requirements.txt │ └── nion_experimental_4dtools │ │ ├── 4d_dark_correction.png │ │ ├── CenterOfMass4D.py │ │ ├── ComputationUI.py │ │ ├── DarkCorrection4D.py │ │ ├── DataCache.py │ │ ├── FramewiseDarkCorrection.py │ │ ├── ImageChooser.py │ │ ├── Map4D.py │ │ ├── Map4DRGB.py │ │ ├── README.md │ │ ├── __init__.py │ │ ├── __pycache__ │ │ ├── CenterOfMass4D.cpython-39.pyc │ │ ├── ComputationUI.cpython-39.pyc │ │ ├── DarkCorrection4D.cpython-39.pyc │ │ ├── DataCache.cpython-39.pyc │ │ ├── FramewiseDarkCorrection.cpython-39.pyc │ │ ├── ImageChooser.cpython-39.pyc │ │ ├── Map4D.cpython-39.pyc │ │ ├── Map4DRGB.cpython-39.pyc │ │ └── __init__.cpython-39.pyc │ │ └── framewise_dark_correction.png └── T2-Data Visualization with NION Swift.pdf ├── Tutorial 3 - Diffraction Simulation ├── Figures │ ├── BilayerMoS2_4.png │ ├── Figures.pptx │ ├── GoldLatticeTable_2.png │ ├── GoldUnitCell_Comparisons5.png │ ├── HowToMuSTEM_2.png │ ├── MoS2_DiffImg_Pratiti.jpg │ ├── MoS2_DiffImg_Pratiti_2.jpg │ ├── MoS2_DiffImg_Pratiti_3.jpg │ ├── MoS2_Supercell.png │ ├── MoS2_Vs_Graphene.png │ ├── MoS2_brokensymmetry4.png │ ├── MonolayerMoS2_xtl.png │ ├── MonolayerMoS2_xtl_border.png │ ├── STO_001.png │ ├── Si_z=0011_A_LOG_LUT-Fire.png │ ├── Si_z=0011_A_LOG_LUT-Fire.tif │ ├── Si_z=0510_A_LOG_LUT-Fire.png │ ├── Si_z=0510_A_LOG_LUT-Fire.tif │ ├── Si_z=0910_A_LOG_LUT-Fire.png │ ├── Si_z=0910_A_LOG_LUT-Fire.tif │ ├── Silicon110_2.png │ ├── Silicon110_ForbiddenReflections_2.png │ ├── Silicon_z=898A_CBED_LUT-fire_Crop150x150_LOG.png │ ├── Silicon_z=898A_CBED_LUT-fire_Crop150x150_LOG.tif │ ├── Supercell_All3_2.png │ └── Zinc_Structure.png ├── Manuals │ ├── UsingVesta.pdf │ └── muSTEM_manual.pdf ├── MuSTEM_methods.py ├── T3_DiffractionSimulation_VM.ipynb └── user_input.txt ├── Tutorial 4 - Spectroscopy ├── MCR_Functions.py ├── T4-EELS with NION Swift.pdf ├── T4a - Basic EELS Processing.ipynb ├── T4b - Advanced EELS Processing.ipynb └── eels.py ├── Tutorial 5 - 4D STEM ├── PEMSS 2021-T5_4DSTEM.pdf ├── T5-4DSTEM.ipynb └── fun.py ├── Tutorial 6 - Ptychography ├── Ptycho_notebook.ipynb └── ePIE_code │ └── ptycho_recon │ ├── __init__.py │ ├── __pycache__ │ ├── browser.cpython-38.pyc │ ├── filters.cpython-38.pyc │ ├── pie_mixed_states.cpython-38.pyc │ ├── postProcess.cpython-38.pyc │ ├── probe.cpython-38.pyc │ ├── ptycho.cpython-38.pyc │ ├── utility_function.cpython-38.pyc │ └── utility_function_recon.cpython-38.pyc │ ├── browser.py │ ├── fft_shift.py │ ├── filters.py │ ├── pie_mixed_states.py │ ├── postProcess.py │ ├── probe.py │ ├── ptycho.py │ ├── utility_function.py │ └── utility_function_recon.py └── Tutorial 7 - Registration ├── T7_atom_finding.ipynb ├── T7_registration.ipynb └── T7_registration_and_atom_finding.pdf /Installation and Dependencies.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/paradimdata/Cornell_EM_SummerSchool_2021/HEAD/Installation and Dependencies.pdf -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/paradimdata/Cornell_EM_SummerSchool_2021/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/paradimdata/Cornell_EM_SummerSchool_2021/HEAD/README.md -------------------------------------------------------------------------------- /Tutorial 0 - 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