SIM Pattern Generator

An ImageJ plugin for generating and overlaying Structured Illumination Microscopy (SIM) interference patterns onto images. Useful for simulating SIM illumination conditions and testing reconstruction pipelines.

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Table of Contents

• Overview
• Requirements
• Installation
• Usage
• Parameters
• Buttons
• Output

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Overview

Structured Illumination Microscopy works by projecting sinusoidal interference patterns onto a sample at multiple angles and phases. This plugin lets you:

• Overlay a customizable sinusoidal SIM pattern onto any open ImageJ image
• Interactively tune angle, phase, spatial frequency, and modulation depth
• Export a standalone pattern image for the current settings
• Generate a full 9-image SIM stack (3 angles × 3 phases) suitable for testing SIM reconstruction algorithms

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Requirements

• ImageJ 1.x or Fiji (recommended)
• Java 8 or later (bundled with Fiji)

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Installation

1. Download SIM_Pattern_Tool.java (or compile it to SIM_Pattern_Tool.class).
2. Place the .java file in your ImageJ plugins/ directory.
3. In ImageJ, go to Plugins → Compile and Run and select the file, or restart ImageJ/Fiji — the plugin will appear under the Plugins menu automatically.

Tip: If you are using Fiji, dropping the file into Fiji.app/plugins/ and restarting is all you need.

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Usage

1. Open an image in ImageJ (File → Open).
2. Launch the plugin via Plugins → SIM Pattern Tool.
3. A control panel appears with editable fields for each parameter.
4. Adjust the values and click Update Pattern to preview the overlay on your image.
5. Use the export buttons to save patterns for further analysis.

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Parameters

Parameter	Range	Default	Description
Angle	0 – 180°	0°	Orientation of the sinusoidal fringe pattern
Phase	0 – 360°	0°	Phase offset of the fringe pattern along its propagation axis
Spatial Frequency	0.1 – 10	3.5	Spatial frequency of the fringes (cycles per unit length, where 1 unit = 0.1 µm pixel size)
Modulation	0 – 1	0.3	Contrast/depth of the sinusoidal modulation (0 = no pattern, 1 = full contrast)

The pattern intensity at each pixel is computed as:

I(x, y) = 0.5 × (1 + m × cos(2π(kx·X + ky·Y) + φ))

where m is modulation, kx/ky are the frequency components along x and y derived from the angle, and φ is the phase offset. Coordinates are centered on the image and scaled by the pixel size (0.1 µm/px).

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Buttons

Update Pattern

Recalculates the sinusoidal pattern with the current parameter values and overlays it onto the original image using additive blending. The original image is preserved internally — only the display is modified.

Export Current Pattern

Generates a standalone 32-bit float grayscale image of the current pattern (without the original image underneath) and opens it as a new ImageJ window titled "Current SIM Pattern".

SIM Test Patterns (3 angles × 3 phases)

Generates a 9-slice ImageJ stack covering the standard SIM acquisition scheme:

Slice	Angle	Phase
1	0°	0°
2	0°	120°
3	0°	240°
4	60°	0°
5	60°	120°
6	60°	240°
7	120°	0°
8	120°	120°
9	120°	240°

The stack opens as "SIM Test Patterns (3 angles × 3 phases)" and uses the spatial frequency and modulation values currently entered in the panel.

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Output

All exported images are 32-bit floating-point processors with values in the range [0, 1], suitable for direct use in SIM reconstruction pipelines or further processing in ImageJ/Fiji.

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