JIMS’ Immobilized Microscopy Suite (JIM)

JIM is a collection of programs designed to simplify the quantitation of in vitro TIRF microscopy experiments. In particular, it is designed to analyze experiments where a substrate is immobilized on the surface of a coverslip before fluorescent reagents are bound to the substrate.

Check out the Getting Started section for further information, including how to install the project.

Contents

• Installation
  • Downloading JIM
  • Prerequisites
  • ImageJ Installation
• Getting Started
  • Running JIM
    • Matlab
    • Python
    • ImageJ
  • Colour Blind Settings
    • Matlab
    • ImageJ
• Generate Traces Parameters
  • File selection
  • Organise Channels
    • Channel Transformation
  • Align Channels and Calculate Drifts
    • Automatic Channel Alignment
    • Manual Channel Alignment
  • Make Sub-Average
  • Detect Particles
    • Filters
  • Additional Background Detection
  • Expand Regions
  • Calculate Traces
  • View Traces
  • Select Batch Files
  • Copy Generated Traces
• Basic C++ Programs
  • Tiff Channel Splitter
  • Align Channels
  • Mean of Frames
  • Expand Shapes
  • Calculate Traces
• Output File Formats
  • CSVs
    • Drift Correction
    • Channel to Channel Alignment
    • ROI Positions
    • Measurements
    • Traces
  • Tiffs
• Jimbob
  • Jimbob Limitations
  • Installing Jimbob
  • Parameters
• Tutorial 1 - Single Channel Trace Generation
  • 0) Import Parameters
  • 1) Select Input File
  • 2) Organise Channels
  • 3) Align/Drift Correct
    • (Optional) Max Shift Example
    • (Optional) Calculating the Accuracy of Drift Correction
  • 4) Make Sub-Average
    • (Optional) Detection Using a Maximum Projection
  • 5) Detect Particles
  • 6) Additional Backgrounds
  • 7) Expand Shapes
  • 8) Calculate Traces
  • 9) View Traces
  • Final Parameters
• Tutorial 2 - Generating Multi-Channel Traces
  • 0) Import Parameters
  • 1) Select Input File
  • 2) Organise Channels
  • 3) Align/Drift Correct
    • (Optional) Calculating the Accuracy of Drift Correction
    • (Optional) Potential pitfalls of Channel Alignment
  • 4) Make Sub-Average
  • 5) Detect Particles
  • 6) Additional Backgrounds
  • 7) Expand Shapes
  • 8) Calculate Traces
  • 9) View Traces
  • 10) Export Trace
  • Final Parameters
• Tutorial 3 - Photobleaching
  • Basic Experimental Setup
  • Analysing Using JIM
  • Generating Traces
    • 0) Import Parameters
    • 1) Select Input File and Create a Folder for Results
    • 2) Organise Channels
    • 3) Drift Correct
    • 4) Make a Sub-Average of the Image Stack for Detection
    • 5) Detect Particles
    • 6) Additional Background
    • 7) Expand Regions
    • 8) Calculate Traces
    • 9) View Traces
    • 10) Extract Trace
    • 11) Detect files for batch
    • 12) Batch Analyse
  • Single-Molecule Photobleaching Analysis of Traces
    • 1) Select Input Folder

Indices and tables

• Index

• Module Index

• Search Page