BASTet: Berkeley Analysis and Storage Toolkit Documentation
Introduction
Converting Files at NERSC and Making them Accessible
Making a converted file accessible to OpenMSI (Private)
Changing file permissions:
convertToOMSI
: Usage and Options
Integrating new file formats
Developing a file reader
Integrating the file reader with OpenMSI
Developing a new Analysis for BASTet
Wrapping a function: The quick-and-dirty way
Writing a new analysis class for BASTet – Part 1: Overview
Writing a new analysis class for BASTet – Part 2: Analysis Template
Writing a new analysis class for BASTet – Part 3: Customizing core features
Defining and Executing Analysis Workflows
Step 1: Create the analysis tasks:
Step 2: Define analysis inputs:
Step 3: Execute
Example: Normalizing an image
Workflow Tools
Workflow Scripts
Developer Notes
Building the online documentation
OMSI Data Format
Data Layout
Accessing OMSI data files
Convert Mass Spectrometry Imaging Data to OMSI (HDF5) format
HDF5 I/O Performance
Test Platforms
Test Cases
Dataset Layout
Chunking: Part 1
Chunking: Part 2
Compression
Local Scalability: Multi-processing
Discussion
omsi Package
Subpackages
BASTet: Berkeley Analysis and Storage Toolkit Documentation
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omsi Package
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tools Package
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tools.experimental Package
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tools.experimental Package
¶
tools.experimental
Package
¶
Collection of experimental tools and tools under development.