Welcome to LLSpy’s documentation!

LLSpy: Lattice light-sheet post-processing utility

Copyright © 2017 Talley Lambert, Harvard Medical School.

LLSpy is a python library to facilitate lattice light sheet data processing. It extends the cudaDeconv binary created in the Betzig lab at Janelia Research Campus, adding features that auto-detect experimental parameters from the data folder structure and metadata (minimizing user input), auto-choose OTFs, perform image corrections and manipulations, and facilitate file handling.

Table of Contents:

• Introduction
  • Overview
    • 1. Graphical User Interface
    • 2. Command Line Interface
    • 3. Interactive data processing in a python console
  • Features of LLSpy
  • Requirements
  • Installation
  • Setup
    • OTF Directory
    • How does LLSpy pick the OTF to use?
    • Flash4.0 Calibration
    • Channel Registration
  • Data Structure Assumptions
    • Filename Parsing
    • Script-editor datasets
  • Known Issues & Bug Reports
• Graphical User Interface
  • Menu Bar
  • Toolbar
  • Process Tab
    • Folder Queue ListBox
    • Pre-Processing
    • Deskew/Deconvolution/Saving
    • Post-Processing
  • Preview Button
  • Process Button
  • Config Tab
    • Use bundled cudaDeconv Binary
    • cudaDeconv binary
    • OTF directory and OTF auto-selection
    • Generating Camera Calibration File
    • Reprocess folders that have already been processed
    • Save MIP Folder during “Reduce to Raw”
    • Warn when quitting with unprocessed items
    • Preview Type
    • Watch Directory (experimental)
    • Error reporting Opt Out
  • Log Tab
  • Progress and Status Bar
• Command Line Interface
• Developer Interface
  • Main Functions
  • Main Classes
    • LLS directory
    • cudaDeconv wrapper
    • *Settings.txt parser
  • Wrapped CUDA functions
  • Exceptions
  • Schema
• LLSpy Camera Corrections
  • Synchronous readout mode
    • After Deskewing…
  • Camera Characterization and Correction
  • LLSpy Carrover Correction
    • Camera Calibration in LLSpy
    • Applying the Correction in LLSpy
• Channel Registration
  • Transformation Modes
    • LLSpy Registration File
    • A Typical Workflow

Indices and tables

• Index
• Module Index
• Search Page