SEM Image Analysis Platform

ChemFitX provides an online SEM image analysis workflow for researchers working with scanning electron microscopy images of particles, powders, catalysts, coatings, porous materials, nanomaterials and other microstructured or nanostructured samples. The platform combines calibrated image measurements, morphology tools, automated particle segmentation, particle-size statistics, size-distribution plots and export functions in one browser-based workspace.

Upload an SEM image, calibrate the spatial scale from a visible scale bar or a known pixel size, and then perform manual measurements or automated particle analysis. Manual tools support distances, diameters, areas, perimeters, angles and custom shapes, while the automated workflow can segment bright or dark particles and report equivalent circular diameter, major and minor axes, aspect ratio, circularity, area fraction and particle-size distributions.

The SEM image is read and analyzed locally in your web browser by this application. The uploaded microscopy file is not sent to ChemFitX servers during the analysis.

What the SEM Image Analysis Platform Can Do

Import SEM images in TIFF/TIF, PNG, JPG/JPEG and BMP formats.
Calibrate image scale from a visible scale bar with a known physical length.
Use direct unit-per-pixel calibration when a validated pixel size is already known.
Measure lines and arrows for calibrated distance or length.
Measure circles for radius, diameter, area and circumference.
Measure ellipses for two radii, area and approximate perimeter.
Measure rectangles for width, height, area and perimeter.
Measure triangles for side lengths, area and perimeter.
Measure polygons for area, perimeter and number of vertices.
Measure angles in degrees.
Add point, cross and arrow annotations to microscopy images.
Apply display-only brightness, contrast and threshold adjustments for visual inspection.
Automatically segment particles using Otsu, adaptive-local-mean or manual thresholding.
Analyze bright particles on a darker background or dark particles on a brighter background.
Filter segmented objects by minimum and optional maximum particle area.
Apply morphological opening, closing or opening-plus-closing to the binary segmentation mask.
Optionally exclude particle objects touching the image border.
Display a particle overlay and optional particle IDs for visual verification.
Report particle count, mean ECD, median ECD, ECD standard deviation, accepted area fraction, mean circularity and mean aspect ratio.
Generate distributions for ECD, major axis, minor axis, area, circularity or aspect ratio.
Export particle measurements separately to CSV or Excel.
Generate statistics and a size-distribution histogram from manually drawn measurement objects.
Pan, zoom, rotate, flip, center and view the SEM image in fullscreen mode.
Customize measurement-line color, transparency, width and line style.
Export an annotated image and measurement data in Excel, CSV or JSON formats.

Supported SEM Images and Analysis Requirements

Supported image formats

The platform accepts TIFF/TIF, PNG, JPG/JPEG and BMP images. For quantitative measurements, use the original SEM image whenever possible. Unnecessary resizing, interpolation, screenshots or lossy compression can change apparent feature dimensions or weaken boundaries used for segmentation.

A valid spatial calibration

Physical dimensions require a valid image scale. ChemFitX can calculate the scale from a visible scale bar or use a known physical pixel size. Without calibration, measurement and automated-particle dimensions remain in pixel units.

Suitable particle contrast

Automated particle analysis works by segmenting grayscale contrast. The selected particle polarity, thresholding method and cleanup settings should separate the structures of interest from the background as consistently as possible. Always inspect the overlay before treating the numerical results as a particle population.

Scale Calibration for SEM Measurements

Scale-bar calibration

To calibrate from a scale bar, choose the scale-calibration tool and draw a line across the full visible bar. Enter the known scale-bar length and select its unit. ChemFitX calculates the number of image pixels per physical unit and then recalculates existing measurements using that calibration.

Supported scale units include nm, micrometers, millimeters, centimeters and angstroms. The measured line should match the printed scale bar as closely as possible because any calibration error propagates directly into lengths, areas and particle-size results.

Direct pixel calibration

When a validated pixel size is already known, the direct calibration option can be used instead of measuring a printed scale bar. Enter the physical size represented by one pixel and choose nm/pixel, micrometers/pixel, angstroms/pixel or mm/pixel.

Do not reuse a scale after resizing an image

A physical pixel calibration is valid only for the image dimensions to which it applies. If an SEM image is resized after acquisition or after a scale bar was generated, the original pixel calibration should not be reused unless the scaling factor is correctly accounted for.

Manual SEM Measurement Tools

Line and arrow measurements

Line and arrow tools report calibrated length. They are useful for particle dimensions, layer thicknesses, pore widths, feature spacing and other direct distances that can be represented by two endpoints.

Circle measurements

A circular measurement reports radius, diameter, area and circumference. This is most appropriate when the feature can reasonably be represented by a circle. For irregular particles, the automated ECD or a polygonal measurement may be more informative.

Ellipse measurements

The ellipse tool reports the two ellipse radii, area and an approximate perimeter. It can be useful for elongated or anisotropic objects when a simple elliptical representation is scientifically appropriate.

Rectangle, triangle and polygon measurements

Rectangles provide width, height, area and perimeter. Triangles provide side lengths, area and perimeter. Polygons provide area, perimeter and the number of vertices. Polygon measurements are useful when the boundary of an irregular region can be manually traced more meaningfully than with a simple geometric shape.

Angle measurements

The angle tool calculates the included angle defined by three selected points and reports the result in degrees. This can support measurements of faceting, intersections, branching features or orientation relationships visible in the image plane.

Automated SEM Particle Size Analysis

The automated particle workflow converts the original decoded image to grayscale and creates a binary particle mask according to the selected segmentation settings. Connected foreground pixels are grouped into particle objects, after which size and morphology descriptors are calculated for accepted objects.

Otsu automatic thresholding

Otsu thresholding automatically selects a global grayscale threshold from the image histogram. It can work well when foreground particles and background form reasonably distinct intensity populations, but it may be less suitable when illumination or detector contrast varies strongly across the field of view.

Adaptive local-mean thresholding

Adaptive thresholding compares each pixel with the mean intensity of a local window and an adjustable offset. This can be useful when background intensity varies spatially. The window size and offset should be chosen carefully because they influence the size and continuity of segmented objects.

Manual thresholding

Manual thresholding gives direct control over the grayscale cutoff. It is useful when the user wants a fixed threshold for a particular image, but the selected value should be justified and the resulting overlay inspected for missed particles, merged objects and false positives.

Bright and dark particle polarity

ChemFitX supports both bright particles on a darker background and dark particles on a brighter background. Choosing the wrong polarity inverts the intended foreground-background interpretation and can produce meaningless particle statistics.

Area filtering and border exclusion

Minimum and optional maximum area filters can remove very small objects or excessively large connected regions from the accepted particle population. Particles touching the image border can also be excluded so that truncated objects do not contribute incomplete size measurements.

Morphological cleanup

The segmentation mask can be processed with morphological opening, closing, or opening followed by closing. Opening can help remove small isolated foreground specks, while closing can fill small gaps or discontinuities. These operations change the segmented mask and therefore can change the measured particle population, so the processed overlay should always be reviewed.

Touching and agglomerated particles

This SEM implementation uses connected foreground regions as particle objects and does not automatically apply watershed separation. Touching or agglomerated particles can therefore be detected as a single connected object. If this occurs, adjust segmentation settings, analyze a more suitable image region, or use a method specifically designed for particle separation.

Particle Size and Morphology Parameters

Equivalent circular diameter (ECD)

Equivalent circular diameter is the diameter of a circle having the same segmented area as the detected object. ChemFitX calculates ECD from the accepted particle area. ECD provides a convenient single-number size descriptor for irregular particles, but it does not mean that the particle is physically circular.

Major and minor axes

Major and minor axes are moment-based ellipse estimates derived from the spatial distribution of pixels within each connected object. They provide an approximate description of particle elongation and are not the same as manually fitted Feret diameters.

Aspect ratio

Aspect ratio is calculated from the estimated major and minor axes. Values closer to 1 indicate a more equiaxed ellipse-like shape, while larger values indicate greater elongation. Interpretation remains dependent on segmentation quality and the suitability of an ellipse-like representation.

Circularity

Circularity is calculated from particle area and perimeter using 4πA/P² and is limited to a maximum value of 1 in the implementation. Values nearer 1 indicate a more compact circular outline, while smaller values can indicate elongation, irregularity or a rough segmented boundary.

Particle area fraction

The accepted area fraction is the percentage of image pixels assigned to accepted particle objects after segmentation and filtering. It is a two-dimensional image-area fraction, not automatically a three-dimensional volume fraction or a material porosity measurement.

Orientation, centroid and perimeter in exports

Particle export data also include perimeter, image-plane orientation, centroid coordinates and whether the object touches the image edge. These values can support downstream filtering or plotting, but their physical interpretation depends on the segmented boundary and image geometry.

Particle Size Distribution and Population Statistics

After particle segmentation, ChemFitX reports the particle count together with mean ECD, median ECD and sample standard deviation of ECD. The distribution plot can be switched among equivalent circular diameter, major axis, minor axis, particle area, circularity and aspect ratio.

The histogram is a descriptive summary of the particles accepted by the current segmentation settings. A scientifically representative particle-size distribution also depends on image selection, magnification, field-of-view sampling, particle overlap, segmentation quality and the number of particles analyzed.

Manual Measurement Statistics and Histogram

Manual measurement objects are summarized separately from the automated particle population. The platform reports the number of measurable objects, mean size, standard deviation, minimum size and maximum size from the primary linear dimensions available in the manually drawn shapes.

A separate manual size-distribution histogram is generated from these primary dimensions. Because different shape types can represent different physical quantities, combine manual measurements into one statistical set only when they correspond to the same scientifically defined size parameter.

Display Adjustments and Image Navigation

Brightness, contrast and threshold sliders are provided for visualization. In this platform, automated particle analysis uses the original decoded image pixels rather than the display-adjusted appearance unless the analysis is explicitly re-run with changed segmentation settings. This separation helps prevent visual enhancement from being confused with the numerical particle mask.

The image workspace includes select/edit, pan, zoom in, zoom out, reset zoom, rotate, horizontal flip, vertical flip, center, fullscreen, undo and redo controls. Cursor readouts provide image X/Y position and grayscale information during inspection.

Measurement and Annotation Customization

Individual measurement lines can be customized by color, transparency, width and solid, dashed or dotted line style. Annotation font size, font family and text color can also be adjusted. These controls are intended for clear presentation and do not change the underlying numerical measurements.

How to Use the ChemFitX SEM Image Analysis Tool

Upload an SEM image in TIFF/TIF, PNG, JPG/JPEG or BMP format.
Inspect the image and confirm that the structures to be measured are clearly resolved.
Calibrate the scale by measuring the full scale bar and entering its known length, or enter a validated direct pixel calibration.
Use the manual measurement tools when individual distances, diameters, areas, perimeters or angles are required.
Use the display controls only as needed to improve visual inspection; do not treat display enhancement as a replacement for segmentation validation.
For automated particle analysis, choose Otsu, adaptive or manual thresholding and select the correct particle polarity.
Set minimum and maximum area filters and optional morphological cleanup according to the structures visible in the image.
Decide whether particles touching the image border should be excluded, then run Analyze Particles.
Inspect the particle overlay carefully. If particles are missed, falsely detected or merged, revise the segmentation settings and repeat the analysis.
Review particle count, ECD statistics, area fraction, circularity, aspect ratio, the selected size-distribution histogram and the particle table.
Compare measurements across images only when image acquisition, calibration, sampling and segmentation procedures are sufficiently consistent.
Export the annotated image and/or numerical measurements to the required format.

Interpreting SEM Particle Analysis Results

Mean versus median particle size

The mean ECD is sensitive to very large or very small segmented objects, while the median ECD represents the middle of the accepted particle population. Reporting both can help reveal when the distribution is strongly skewed.

Standard deviation

The reported ECD standard deviation describes the spread of accepted ECD values in the analyzed image. It does not by itself establish confidence intervals for the material population because image selection and sampling variability are separate issues.

Area fraction

Area fraction reports how much of the analyzed image is occupied by accepted segmented particle pixels. It is useful as a two-dimensional descriptor but should not automatically be equated with mass fraction, volume fraction or porosity.

Circularity and aspect ratio

Circularity and aspect ratio are morphology descriptors derived from the segmented two-dimensional projection. Their values can change when thresholding, morphology cleanup, image resolution or particle overlap changes the detected boundary.

Exporting SEM Analysis Results

Annotated image

The image-export function can save the microscopy image with measurement labels included or omitted. Export font size, font family and font weight can be adjusted before generating the image.

Excel

The general Excel export stores manual measurement results and, when automated particle analysis has been run, includes a separate particle worksheet. The dedicated particle Excel export also provides particle-level measurements together with a summary of particle count, accepted area fraction, segmentation threshold and active size unit.

CSV

The general CSV export stores manual measurement results. A separate particle CSV export provides particle ID, area, equivalent circular diameter, major axis, minor axis, perimeter, aspect ratio, circularity, orientation, centroid position and edge-touching status.

JSON

JSON export provides the manually drawn measurement results in a structured format that can be reused programmatically or archived with other analysis records.

Data Privacy and Browser-Based Processing

For this SEM application, the uploaded microscopy image is read and analyzed locally in the browser. The analysis code does not upload the SEM image to ChemFitX servers.

Users should still follow their laboratory or institution policies for unpublished microscopy data, confidential samples, shared computers, browser storage and downloaded analysis files.

Scientific Scope and Limitations

Accurate physical dimensions require a correct scale-bar or direct pixel calibration.
If an image has been resized, a calibration from the original pixel dimensions should not be reused without correcting for the resize factor.
Automated particle results depend on image contrast, thresholding, particle polarity, area filters and morphological cleanup settings.
The automated workflow groups connected foreground pixels into objects; touching or agglomerated particles may therefore be measured as one particle.
This SEM implementation does not automatically perform watershed separation of touching particles.
Equivalent circular diameter is an area-equivalent descriptor and does not imply a circular physical particle.
Major and minor axes are image-moment-based ellipse estimates rather than direct Feret-diameter measurements.
Circularity depends strongly on the segmented perimeter and can be affected by pixelation, noise, magnification and threshold selection.
Area fraction is a two-dimensional accepted-pixel fraction and is not automatically a three-dimensional volume fraction or porosity.
Particles touching the image edge are incomplete observations; the platform can exclude them when the corresponding option is enabled.
Display brightness, contrast and threshold controls are visualization aids and should not be confused with validated quantitative preprocessing.
JPEG compression, screenshots, resampling and aggressive image editing can alter particle edges and should be avoided for quantitative analysis when original data are available.
SEM particle-size distributions are only as representative as the fields of view and particles sampled. Multiple representative images may be required for defensible population statistics.
Two-dimensional SEM projections do not directly provide three-dimensional particle size, thickness or volume without additional assumptions or measurements.
The platform is an analysis aid and does not replace appropriate microscopy acquisition, calibration, segmentation validation or expert interpretation.

Frequently Asked Questions

What is SEM image analysis?

SEM image analysis uses scanning electron microscopy images to measure and describe visible microstructural or particle features such as size, shape, area, spacing and morphology. Quantitative results depend on image calibration, resolution, contrast and a scientifically appropriate analysis method.

Can I measure particle size from an SEM image online with ChemFitX?

Yes. After calibrating the image, you can make manual measurements or run automated particle segmentation and calculate ECD and other morphology descriptors.

Which image formats are supported?

The platform accepts TIFF/TIF, PNG, JPG/JPEG and BMP images.

Do I need to calibrate the SEM image?

Calibration is required for physical units. You can measure a visible scale bar or enter a validated physical pixel size. Without calibration, dimensional results remain in pixels.

Which threshold methods are available for particle analysis?

ChemFitX provides Otsu automatic thresholding, adaptive local-mean thresholding and manual thresholding.

Can the tool analyze both bright and dark particles?

Yes. You can choose bright particles on a darker background or dark particles on a brighter background.

What is ECD?

ECD means equivalent circular diameter. It is the diameter of a circle with the same segmented area as the detected particle.

Does ECD mean my particles are circular?

No. ECD is an area-equivalent size descriptor and can be calculated for irregular particles.

What does circularity mean?

Circularity is calculated from segmented area and perimeter using 4πA/P². Values nearer 1 indicate a more compact circular boundary in the two-dimensional segmentation.

What does aspect ratio mean?

Aspect ratio is based on the moment-derived major and minor axes of the segmented particle. Higher values indicate a more elongated two-dimensional object.

Can ChemFitX separate touching particles automatically?

Not in this SEM implementation. Connected foreground regions are treated as single objects, so touching or agglomerated particles can be merged. The overlay should always be checked visually.

Can I remove very small segmentation artifacts?

Yes. Use the minimum-area filter and, when appropriate, morphological opening. You can also set a maximum area to exclude unusually large connected regions.

Should I exclude particles touching the image border?

For many particle-size analyses, excluding border-touching objects helps avoid incomplete size measurements. The platform provides this option and enables it by default.

Does changing brightness or contrast change the automated particle results?

The display adjustments are intended for visualization. Automated particle analysis uses the original decoded image pixels and changes only when segmentation settings are changed and the analysis is run again.

What statistics are reported for automated particles?

The platform reports particle count, mean ECD, median ECD, sample standard deviation of ECD, accepted area fraction, mean circularity, mean aspect ratio and the threshold used.

Can I plot particle-size distributions?

Yes. The particle histogram can display ECD, major axis, minor axis, area, circularity or aspect ratio distributions.

Can I export individual particle measurements?

Yes. Particle-level results can be exported to CSV or Excel and include size, shape, orientation, centroid and edge-touching information.

Are my SEM images uploaded to ChemFitX?

For this application, the SEM image is read and analyzed locally in the browser and is not uploaded to ChemFitX servers by the analysis code.

Can I export my manual SEM measurements?

Yes. Manual measurements can be exported in Excel, CSV or JSON formats, and the annotated image can also be exported.

Can a single SEM image represent the whole sample?

Not necessarily. A defensible particle-size or morphology distribution may require several representative fields of view, suitable magnification and a consistent sampling strategy.

Scientific References

Goldstein, J. I.; Newbury, D. E.; Michael, J. R.; Ritchie, N. W. M.; Scott, J. H. J.; Joy, D. C. Scanning Electron Microscopy and X-Ray Microanalysis. Springer.
Russ, J. C.; Neal, F. B. The Image Processing Handbook. CRC Press.
Otsu, N. A Threshold Selection Method from Gray-Level Histograms. IEEE Transactions on Systems, Man, and Cybernetics, 1979, 9, 62-66.