GDSC ImageJ Plugins

The GDSC ImageJ plugins are a collection of analysis programs for microscopy images including colocalisation analysis and peak finding. These run as plugins within ImageJ, an image processing and analysis program using Java.

The plugins are easily installed into ImageJ. The library works for Java 11+. This is the java specification used by SciJava for participating projects as of 2026 (see org.scijava:pom-scijava). It is recommended that all ImageJ plugins use this specification to maximise compatibility.

The plugins were developed at the Genome Damage and Stability Centre at the University of Sussex, UK. The source code is hosted on GitHub.

The plugins can be incorporated into ImageJ macros to allow automation of image analysis workflows.

The following plugins are available using the order presented on the ImageJ > Plugins > GDSC menu:

Cells Plugins

The Cells Plugins provide tools for analysis of cells from microscopy images.

Colocalisation Analysis

The Colocalisation Plugins provide various tools to perform colocalisation analysis. The tools include:

• Thresholding for N-dimensional images for signal identification

• Correlation and overlap coefficient analysis

• Colocalisation significance testing

Find Foci

The Find Foci Plugins allow the identification of peak intensity regions within 2D and 3D images. The tools include:

• Automated and semi-automated labelling of peaks

• Comparison of marked points between images

• Optimisation of algorithm parameters

• Batch analysis of images

• Alignment of manually marked points to peak maxima

Thresholding Plugins

The Thresholding Plugins provide various tools for thresholding and mask generation.

Utility Plugins

The Utility Plugins provide various utility tools for image analysis. The tools include:

• Difference of Gaussians and Laplacian of Gaussian filters for contrast enhancement

• Image alignment

• Mask conversion and measurement tools

Contents

• 1. Installation
  • 1.1. Install using ImageJ2/Fiji
  • 1.2. Install using ImageJ version 1
  • 1.3. Toolsets
• 2. ImageJ Plugins Overview
  • 2.1. Usage Tracking
    • 2.1.1. Usage Data
    • 2.1.2. Tracking Identifiers
    • 2.1.3. Performance
    • 2.1.4. User Preferences
    • 2.1.5. Google Analytics Details
• 3. Cells Plugins
  • 3.1. Cell Outliner
    • 3.1.1. Method
    • 3.1.2. Plugin Interface
    • 3.1.3. Output
  • 3.2. Nuclei Outline
    • 3.2.1. Method
    • 3.2.2. Plugin Interface
    • 3.2.3. Results Overlay
    • 3.2.4. Results Table
• 4. Colocalisation Plugins
  • 4.1. Stack Threshold
    • 4.1.1. Image Thresholding
    • 4.1.2. Plugin Interface
  • 4.2. Colocalisation Threshold
    • 4.2.1. Features
    • 4.2.2. Method
      • 4.2.2.1. Step 1: Regression Analysis
      • 4.2.2.2. Step 2: Define Limits
      • 4.2.2.3. Step 3: Iterative Search
    • 4.2.3. Plugin Interface
      • 4.2.3.1. Input Parameters
      • 4.2.3.2. Search Parameters
      • 4.2.3.3. Results Parameters
      • 4.2.3.4. Results Options
    • 4.2.4. Results Table
  • 4.3. CDA
    • 4.3.1. Features
    • 4.3.2. Method
      • 4.3.2.1. Stage 1: Identify Channel Signal
      • 4.3.2.2. Stage 2: Analysis
    • 4.3.3. Plugin Interface
      • 4.3.3.1. Input Parameters
      • 4.3.3.2. Displacement Parameters
      • 4.3.3.3. Options Parameters
      • 4.3.3.4. Results Options
    • 4.3.4. Results Table
  • 4.4. CDA (macro)
  • 4.5. Stack Correlation Analyser
    • 4.5.1. Plugin Interface
    • 4.5.2. Results
  • 4.6. Stack Colocalisation Analyser
    • 4.6.1. Plugin Interface
    • 4.6.2. Results Table
  • 4.7. Particle Overlap
    • 4.7.1. Plugin Interface
    • 4.7.2. Results Table
  • 4.8. Particle Correlation
    • 4.8.1. Plugin Interface
    • 4.8.2. Summary Table
    • 4.8.3. Results Table
    • 4.8.4. Scatter Plot
    • 4.8.5. Object Mask
  • 4.9. Colocated Mask
    • 4.9.1. Plugin Interface
    • 4.9.2. Output
  • 4.10. Batch Processing
    • 4.10.1. Step 1: Record the Macro
    • 4.10.2. Step 2: Prepare Input Files
    • 4.10.3. Step 3: Process Batch Command
    • 4.10.4. Batch Macros
• 5. Find Foci Plugins
  • 5.1. FindFoci
    • 5.1.1. Features
    • 5.1.2. Overview
      • 5.1.2.1. Stage 1: Assign Background
      • 5.1.2.2. Stage 2: Assign Maxima
      • 5.1.2.3. Stage 3: Expand Peaks
      • 5.1.2.4. Stage 4: Merge Peaks
    • 5.1.3. Image Input
      • 5.1.3.1. 32-bit Support
    • 5.1.4. Plugin Interface
      • 5.1.4.1. Mask
      • 5.1.4.2. Background Parameters
      • 5.1.4.3. Search Parameters
      • 5.1.4.4. Peak Merging Parameters
      • 5.1.4.5. Results Parameters
      • 5.1.4.6. Advanced Parameters
    • 5.1.5. Results Table
      • 5.1.5.1. Sorting
  • 5.2. FindFoci GUI
    • 5.2.1. Features
    • 5.2.2. Plugin Interface
      • 5.2.2.1. Preview
      • 5.2.2.2. Java Requirements
  • 5.3. FindFoci Batch
    • 5.3.1. Features
    • 5.3.2. Overview
      • 5.3.2.1. Create the FindFoci Parameters
      • 5.3.2.2. Note on the Parameters
      • 5.3.2.3. Custom Channel, Time Frame and Z-slice Parameters
    • 5.3.3. Plugin Interface
      • 5.3.3.1. Output
      • 5.3.3.2. Multi-thread Mode
  • 5.4. FindFoci Optimiser
    • 5.4.1. Features
    • 5.4.2. Overview
      • 5.4.2.1. Stage 1: Create Reference Foci
      • 5.4.2.2. Stage 2: Run the Optimiser
    • 5.4.3. Result Assessment
    • 5.4.4. Plugin Interface
      • 5.4.4.1. Settings Presets
      • 5.4.4.2. Range and List Fields
      • 5.4.4.3. Initialisation Parameters
      • 5.4.4.4. Search Parameters
      • 5.4.4.5. Peak Merging Parameters
      • 5.4.4.6. Results Parameters
      • 5.4.4.7. Extra Parameters
      • 5.4.4.8. Optimisation Parameters
      • 5.4.4.9. Additional Parameters
    • 5.4.5. Output
      • 5.4.5.1. Result Table
      • 5.4.5.2. FindFoci Images
      • 5.4.5.3. Score Images
  • 5.5. FindFoci Optimiser GUI
    • 5.5.1. Features
    • 5.5.2. Plugin Interface
      • 5.5.2.1. Java Requirements
  • 5.6. FindFoci Optimiser Multi-Image
    • 5.6.1. Features
    • 5.6.2. Input
    • 5.6.3. Method for Combined Ranking
      • 5.6.3.1. Score Conversion
    • 5.6.4. Plugin Interface
    • 5.6.5. Results
      • 5.6.5.1. Result Table
      • 5.6.5.2. Invalid Results
  • 5.7. FindFoci Helper
    • 5.7.1. Features
    • 5.7.2. Overview
    • 5.7.3. Plugin Interface
    • 5.7.4. Workflow
      • 5.7.4.1. Multi-point ROI Mode
      • 5.7.4.2. Initialisation
      • 5.7.4.3. Marking Peaks
      • 5.7.4.4. Moving Peaks
      • 5.7.4.5. Deleting Peaks
      • 5.7.4.6. Point Overlay
      • 5.7.4.7. Saving Results
      • 5.7.4.8. Stopping Point Alignment
    • 5.7.5. Alignment Log
    • 5.7.6. Java Requirements
  • 5.8. FindFoci Settings
  • 5.9. FindFoci Match Calculator
  • 5.10. FindFoci Macro Extensions
    • 5.10.1. getNumberOfPeaks
  • 5.11. Match Calculator
    • 5.11.1. Features
    • 5.11.2. Overview
      • 5.11.2.1. Match Algorithm
      • 5.11.2.2. Height Analysis
    • 5.11.3. Plugin Interface
      • 5.11.3.1. Extra Parameters
    • 5.11.4. Results Table
    • 5.11.5. Unmatched Results Table
    • 5.11.6. Match Table
    • 5.11.7. Overlay
  • 5.12. File Match Calculator
  • 5.13. Point Aligner
    • 5.13.1. Features
    • 5.13.2. Overview
      • 5.13.2.1. Alignment Algorithm
      • 5.13.2.2. Minimum Peak Height Limit
      • 5.13.2.3. Alignment Results
    • 5.13.3. Plugin Interface
    • 5.13.4. Results Table
    • 5.13.5. Alignment Log
    • 5.13.6. Unaligned Images
    • 5.13.7. Overlay
  • 5.14. Point Extractor
    • 5.14.1. Features
    • 5.14.2. Overview
    • 5.14.3. Plugin Interface
    • 5.14.4. Creating a 3D Coordinate File
  • 5.15. Spot Distance
  • 5.16. Spot Pairs
  • 5.17. Mask Divider
  • 5.18. Double Mask Divider
  • 5.19. Mask Analyze Particles…
  • 5.20. Mask Analyze Channels…
  • 5.21. Spot Density
  • 5.22. Mask Object Dimensions
  • 5.23. Assign Foci to Objects
    • 5.23.1. Features
    • 5.23.2. Overview
    • 5.23.3. Plugin Interface
    • 5.23.4. Results
  • 5.24. Assign Foci to Clusters
    • 5.24.1. Features
    • 5.24.2. Overview
    • 5.24.3. Plugin Interface
    • 5.24.4. Clustering Algorithm
    • 5.24.5. Results
  • 5.25. Translocation Finder
  • 5.26. Translocation Finder (Tool)
  • 5.27. Spot Radial Intensity
  • 5.28. Spot Pair Distance
  • 5.29. Object Foci Depth
  • 5.30. Foci Neighbour Analysis
  • 5.31. Binary Scoring Statistics
    • 5.31.1. Jaccard
    • 5.31.2. Recall
    • 5.31.3. Precision
    • 5.31.4. F-score
    • 5.31.5. Defining the Actual or Predicted Points
• 6. Thresholding Plugins
  • 6.1. Global Threshold
    • 6.1.1. Plugin Interface
    • 6.1.2. Output
  • 6.2. Multi-Threshold
    • 6.2.1. Plugin Interface
    • 6.2.2. Output
  • 6.3. Mask Creator
    • 6.3.1. Plugin Interface
    • 6.3.2. Output
  • 6.4. Edge Mask
    • 6.4.1. Plugin Interface
    • 6.4.2. Output
  • 6.5. Apply Mask
    • 6.5.1. Plugin Interface
    • 6.5.2. Output
  • 6.6. Skeleton Analyser
    • 6.6.1. Plugin Interface
    • 6.6.2. Output
  • 6.7. Thread Analyser
    • 6.7.1. Plugin Interface
    • 6.7.2. Results Table
  • 6.8. Foreground Analyser
    • 6.8.1. Plugin Interface
    • 6.8.2. Results Table
  • 6.9. Threshold Outliner
    • 6.9.1. Plugin Interface
    • 6.9.2. Output
• 7. Utility Plugins
  • 7.1. Contrast Enhancer
  • 7.2. Difference of Gaussians
    • 7.2.1. Plugin Interface
    • 7.2.2. Output
  • 7.3. Laplacian of Gaussian
    • 7.3.1. Plugin Interface
    • 7.3.2. Output
  • 7.4. Align Images
    • 7.4.1. Plugin Interface
    • 7.4.2. Output
  • 7.5. Align Images FFT
    • 7.5.1. Plugin Interface
    • 7.5.2. Output
  • 7.6. Align Stacks
    • 7.6.1. Plugin Interface
  • 7.7. Image Scaler
    • 7.7.1. Plugin Interface
  • 7.8. Spot Analyser
    • 7.8.1. Plugin Interface
    • 7.8.2. Results Table
  • 7.9. HSB Picker
    • 7.9.1. Plugin Interface
  • 7.10. HSB Filter
    • 7.10.1. Plugin Interface
    • 7.10.2. Output
  • 7.11. Spot Separation
    • 7.11.1. Plugin Interface
    • 7.11.2. Results Table
  • 7.12. Z Project extra…
  • 7.13. Intensity Analysis
    • 7.13.1. Plugin Interface
    • 7.13.2. Results
  • 7.14. Measure 3D
    • 7.14.1. Results Table
  • 7.15. Scale Space
    • 7.15.1. Plugin Interface
    • 7.15.2. Output
  • 7.16. FRAP Analysis
    • 7.16.1. Method
    • 7.16.2. Plugin Interface
    • 7.16.3. Results
  • 7.17. Mask to ROI
    • 7.17.1. Plugin Interface
    • 7.17.2. Output
  • 7.18. Mask to Border
    • 7.18.1. Plugin Interface
    • 7.18.2. Output
  • 7.19. Mask Overlap
    • 7.19.1. Plugin Interface
    • 7.19.2. Output
• 8. References

Index

• Index

• Search Page

Issues

Please file a bug report on GitHub.