MicroMeasure

Web-Based Image Analysis and Measurement Tool

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If you use MicroMeasure in academic work:

Overview

MicroMeasure is a browser-based image analysis application designed for quantitative measurements of scientific images, particularly microscopy images such as scanning electron microscopy (SEM) micrographs. The application provides intuitive tools for measuring length, angle, area, particle size, and hole size, without requiring software installation.

MicroMeasure is inspired by widely used scientific image analysis platforms (e.g., ImageJ) but optimized for fast, web-based workflows and educational use.

Intended Users

MicroMeasure is intended for:

• Researchers and laboratory personnel
• Graduate and undergraduate students
• Educators and instructors
• Materials science, physics, chemistry, biology, and engineering users

Quick Start

1. Load an image - Click "Load Image" or drag & drop an image file
2. Set the scale - Click "Set Scale", draw a line of known length, then enter the real-world measurement
3. Make measurements - Use the tabs to measure lengths, angles, areas, particles, or holes
4. Export results - Use the Copy TSV / Download CSV buttons at the bottom of each measurement tab

Scale Calibration

Before making real-world measurements, you must calibrate the scale:

• Click the Set Scale button in the image controls
• Click two points on a feature of known length (e.g., a scale bar)
• Enter the known length and select the unit (nm, μm, mm)
• Click Save Scale to apply calibration
• All measurements will now show both pixel and real-world values
• Use Reset to clear calibration if needed

Length Measurements

Measure distances between two points:

• Switch to the Length tab
• Click two points on the image to create a measurement
• Each measurement is labeled (L1, L2, etc.)
• Use the Edit (✏️) button to adjust endpoints by dragging
• Use the Eye (👁) button to show/hide measurements
• Click the × button to delete a measurement

Angle Measurements

Measure the angle formed by two rays meeting at a vertex:

• Switch to the Angle tab
• Click three points on the image
• The second point is the vertex (middle point)
• Each angle is labeled (Ang1, Ang2, etc.) and reported in degrees (deg)
• Use the Edit (✏️) button to adjust by dragging any of the three points, then Save Changes or Cancel
• Use the Eye (👁) button to show/hide, and × to delete

Area Measurements

Measure areas using either polygons or ovals:

• Switch to the Area tab
• Use Polygon mode to click points and create a polygon outline
• Click Close Polygon when you have 3+ points, or double-click to close
• Use Oval mode to click and drag a bounding box for the oval
• Each area is labeled (A1, A2, etc.)
• Use Edit to adjust polygon vertices or move/resize an oval
• While editing a polygon, click or tap an edge to add a point
• Delete polygon points with right-click on desktop or double-tap on touch/pen devices
• Use Eye to show/hide, × to delete

Particle Analysis

Automatically detect and measure particles:

Region of Interest (ROI)

• Click Select ROI to restrict analysis to a specific region
• Click and drag to draw a rectangular region
• Click Clear ROI to analyze the full image

Preprocessing Options

• Background subtraction - Removes uneven illumination (rolling ball method)
• Smoothing - Reduces noise using Gaussian or Median filters
• Morphological opening - Removes small noise objects

Thresholding

• Auto (Otsu) - Automatically calculates optimal threshold
• Manual - Adjust threshold slider (0-255)
• Adaptive - Local thresholding for uneven backgrounds
• Select whether particles are bright or dark

Analysis

• Set Min Area to filter out small noise (in real units if calibrated)
• Click Analyze Particles
• View count, mean area, mean ECD (Equivalent Circular Diameter), and size distribution
• Each detected particle is overlaid with a semi-transparent pastel fill that follows the detected shape

🕳️ Hole Analysis

Automatically detect and measure holes/voids in materials:

Region of Interest (ROI)

• Click Select ROI to restrict analysis to a specific region
• Click and drag to draw a rectangular region
• Click Clear ROI to analyze the full image

Preprocessing Options

• Background subtraction - Removes uneven illumination (rolling ball method)
• Smoothing - Reduces noise using Gaussian or Median filters
• Morphological opening - Removes small noise objects

Thresholding

• Auto (Otsu) - Automatically calculates optimal threshold
• Manual - Adjust threshold slider (0-255)
• Adaptive - Local thresholding for uneven backgrounds
• Select whether holes are dark or bright

Analysis

• Set Min Area to filter out small noise (in real units if calibrated)
• Click Analyze Holes
• View count, mean area, mean ECD (Equivalent Circular Diameter), and size distribution
• Each detected hole is outlined in purple on the image

📈 Descriptive Statistics & Histogram

Summarize and visualize your measurements:

• Descriptive Statistics shows mean, median, standard deviation, quartiles, etc.
• Histogram shows the distribution of values (adjust bin count in the histogram window).
• Buttons appear when there is enough data (shown when n ≥ 4 for the selected feature).
• For Length/Area/Particles/Holes, values are shown in pixels until scale is calibrated (then real units are shown).
• Angle is always in degrees and does not require calibration.
• In the histogram window, Particles/Holes can be plotted by ECD or Area (metric selector).

🧭 Navigation & Controls

• Zoom - Use the slider, mouse wheel, or pinch gesture
• Pan - Middle-click drag, Alt+drag, two-finger drag, or use arrow buttons/keys
• Fit to View - Automatically adjusts zoom to fit the image
• Drag & Drop - Drag image files directly onto the canvas

📥 Results & Export

Export data from within each measurement tab:

• Save Image - Export image with all measurements overlaid (PNG)
• Copy TSV - Copy the current tab’s data as tab-separated values (paste into spreadsheets)
• Download CSV - Download the current tab’s data as a .csv file
• Area export note: Area rows include a Shape column so Polygon and Oval measurements stay distinguishable.
• Note: Export buttons appear only when the current tab has at least one measurement/object.
• Reset - Use the reset control to clear measurements and restart

💡 Tips & Tricks

• Always calibrate scale first for accurate real-world measurements
• Use ROI selection to speed up particle/hole analysis on large images
• Try Auto (Otsu) threshold first, then adjust manually if needed
• Adaptive thresholding works best for images with uneven lighting
• Background subtraction is useful for removing gradients in microscopy images
• Increase smoothing to reduce noise, but be careful not to blur features
• Morphological opening removes small speckles without affecting larger particles
• The Save Image button is only enabled when you have measurements on the image

Keyboard Shortcuts

• Arrow Keys - Pan the image
• Mouse Wheel - Zoom in/out
• Alt + Left Click - Pan the image

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