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# ncempy
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A comprehensive Python library for electron microscopy data analysis and simulation. ncempy provides algorithms and routines for image processing, file I/O with various microscopy formats, visualization tools, data evaluation, and specialized EDS tomography reconstruction capabilities for electron microscopy research.
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## Package Information
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- **Package Name**: ncempy
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- **Language**: Python
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- **Installation**: `pip install ncempy`
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## Core Imports
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```python
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import ncempy
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```
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Common usage patterns:
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```python
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import ncempy.io
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import ncempy.algo
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import ncempy.viz
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import ncempy.eval
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# Direct access to main functions
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from ncempy import read, plot
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```
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## Basic Usage
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```python
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import ncempy
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import matplotlib.pyplot as plt
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# Read electron microscopy data files
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data = ncempy.read('microscopy_data.dm3')
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print(f"Data shape: {data['data'].shape}")
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print(f"Pixel size: {data['pixelSize']}")
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# Display the data
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ncempy.plot(data)
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plt.show()
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# Perform image correlation alignment
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import ncempy.algo as algo
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aligned = algo.image_correlate(data['data'], reference_image)
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# Visualize with calibrated axes
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ncempy.viz.im_calibrated(aligned, data['pixelSize'])
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plt.show()
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```
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## Architecture
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ncempy is organized into modular components for maximum reusability:
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- **I/O Module**: Universal file reader supporting multiple microscopy formats (SER, DM3/DM4, EMD, MRC, SMV)
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- **Algorithm Module**: Core image processing, correlation, peak finding, and mathematical functions
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- **Visualization Module**: Plotting utilities optimized for microscopy data with calibrated axes
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- **Evaluation Module**: Analysis tools for stack alignment, line profiles, and ring diffraction
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- **EDS Tomography Module**: Specialized tools for energy-dispersive X-ray spectroscopy tomography reconstruction
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## Capabilities
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### File Input/Output
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Universal file reading and format conversion for multiple electron microscopy file formats including Digital Micrograph, SER, EMD/HDF5, MRC, and SMV files.
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```python { .api }
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def read(filename: str) -> dict: ...
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```
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[File I/O Operations](./file-io.md)
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### Image Processing Algorithms
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Comprehensive image processing capabilities including correlation-based alignment, peak detection, Fourier operations, distortion correction, and mathematical fitting functions.
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```python { .api }
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def image_correlate(image1, image2, **kwargs): ...
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def stack_align(image_stack, **kwargs): ...
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def peakFind2D(image, **kwargs): ...
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def rebin(array, shape_out, **kwargs): ...
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```
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[Image Processing Algorithms](./algorithms.md)
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### Data Visualization
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Specialized plotting functions for electron microscopy data with calibrated axes, FFT displays, interactive stack viewing, and scientific visualization tools.
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```python { .api }
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def plot(data_dict, **kwargs): ...
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def im_calibrated(image, pixel_size, **kwargs): ...
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def imfft(image, **kwargs): ...
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class stack_view: ...
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```
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[Visualization Tools](./visualization.md)
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### Data Evaluation
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Analysis tools for extracting quantitative information from microscopy data including line profiles, ring diffraction analysis, and multi-correlation techniques.
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```python { .api }
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def line_profile(image, start, end, **kwargs): ...
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def multicorr(image_stack, **kwargs): ...
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```
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[Data Evaluation](./evaluation.md)
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### EDS Tomography
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Specialized functionality for energy-dispersive X-ray spectroscopy tomography including preprocessing, reconstruction interface with GENFIRE, and postprocessing tools.
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```python { .api }
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def ExtractSignalsFromEMD(emd_file, **kwargs): ...
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def WriteSignalsToGENFIRE(signals, **kwargs): ...
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def ReadGENFIRESignals(results_file, **kwargs): ...
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```
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[EDS Tomography](./eds-tomography.md)
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### Command Line Tools
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CLI utilities for common tasks including file format conversion and batch processing operations.
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```python { .api }
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# Console script: ncem2png
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def main(): ...
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```
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[Command Line Tools](./command-line.md)
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## Supported File Formats
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- **SER files** (`.ser`) - FEI/Thermo Fisher TIA format
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- **Digital Micrograph files** (`.dm3`, `.dm4`) - Gatan format
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- **EMD/HDF5 files** (`.emd`, `.h5`, `.hdf5`) - Electron Microscopy Dataset format
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- **MRC files** (`.mrc`, `.rec`, `.st`, `.ali`) - Medical Research Council format
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- **SMV files** (`.smv`, `.img`) - Single-image format
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## Dependencies
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- **Core**: numpy>=2, scipy, matplotlib, h5py>=3
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- **Optional**: glob2, genfire, hyperspy, scikit-image, ipyvolume (for EDS tomography)