Welcome to bmiptools’s documentation!

• Introduction
  • Scope
  • Repository
  • How to cite this tool?

Usage:

• Installation and configuration
  • Installation
  • Configuration
• Basic API usage
  • Stack
  • Pipeline
  • Further reading
• Advanced API usage
  • Initialize a plugin
  • Plugin optimization
  • Apply a plugin
  • Get plugin parameters
• GUI usage
  • Run the GUI
  • Load a stack
  • Create and initialize a pipeline
  • Load a pipeline template
  • Apply pipeline and previews
  • Save results
  • Load an existing pipeline
  • Further reading

Plugins:

• General information about plugins
  • What is plugin optimization?
  • Transformation dictionary
  • Available plugins
• Standardizer
  • Transformation dictionary
  • Use case
  • Application example
  • Implementation details
• Histogram matcher
  • Transformation dictionary
  • Use case
  • Application example
  • Implementation details
  • Further details
• Denoiser
  • Transformation dictionary
  • Use case
  • Application example
  • Implementation details
  • Further reading
• Denoiser DNN
  • Transformation dictionary
  • Use case
  • Application example
  • Implementation details
  • Further reading
• Destriper
  • Transformation dictionary
  • Use case
  • Application example
  • Implementation details
  • Further details
• Flatter
  • Transformation dictionary
  • Use case
  • Application example
  • Implementation details
  • Further details
• Decharger
  • Transformation dictionary
  • Use case
  • Application example
  • Implementation details
  • Further details
• Registrator
  • Transformation dictionary
  • Use case
  • Application example
  • Implementation details
  • Further details
• Affine
  • Transformation dictionary
  • Use case
  • Application example
  • Implementation details
  • Further details
• Cropper
  • Transformation dictionary
  • Use case
  • Application example
  • Implementation details
• Equalizer
  • Transformation dictionary
  • Use case
  • Application example
  • Implementation details
  • Further details

Visualization:

• Basic visualization tools in bmiptools
  • Basic slice visualization
  • Compare two slices
  • Visualizing image grey-levels as surface
  • Plot masks on slices
• Change coordinate system
  • Preliminary facts
  • Tool usage
  • Further reading

Developer:

• General conventions
  • The CoreBasic and the global settings
  • General recommendations
• General plugin structure
  • Basic transformation structure
  • Conventions for the plugin construction
• GuiPI: automatic GUI generation for plugins
  • GUI Parameters Information, i.e. GuiPI
  • Guize
• Plugin installation
  • Add and use a new plugin
  • Remove a plugin
• Contribute or Issue report
  • Issue request
  • Integrate custom plugins
  • To do list
• API References

Miscellaneous:

• Basic operations with stacks and pipelines
  • The input stack and its problems
  • Post-processing using bmiptools pipelines
  • Final result
• Create and install a custom plugin
  • An example of custom plugin
  • Plugin installation
• Case of study: destriper optimization
  • The optimization routine
  • Results
• Case of study: decharger optimization
  • The optimization routine
  • Results

Indices and tables

• Index

• Module Index

• Search Page