How can I sharpen SEM images in GIMP to better measure repeating structures?
Asked 3/7/2022
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2 answers
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I need to measure pixel lengths along chains of repeating bead-like structures in scanning electron microscope images for a thesis project. The SEM images are somewhat soft, making it hard to identify suitable chains and measure them consistently. I have access to GIMP and would like suggestions for image processing steps that can improve visibility of the structures for measurement. If there are useful GIMP tools or workflows for both sharpening and extracting measurement points, those would help as well.
Originally by user105273. Source · Licensed CC BY-SA 4.0
user105273
4y ago
2 Answers
4
The quickest way to sharpen things in modern Gimp (2.10):
Filters > Enhance > Wavelet decompose- Then duplicate/triplicate the top layers as needed (
Scale 1,Scale 2)
In addition if you want to do a lot of measures of an image, something that can help:
- Use the Path tool and add anchors on the points of interest:
Then use the path-csv script to export path data to a CSV:
,,,,,,,
Seeds,1,619.5,376.5,619.5,376.5,619.5,376.5
Seeds,1,620.0,385.5,620.0,385.5,620.0,385.5
Seeds,1,621.5,396.0,621.5,396.0,621.5,396.0
Seeds,1,622.0,403.0,622.0,403.0,622.0,403.0
Seeds,1,623.0,411.0,623.0,411.0,623.0,411.0
Seeds,1,623.0909090909091,418.1818181818182,623.0909090909091,418.1818181818182,623.0909090909091,418.1818181818182
Seeds,1,624.0,426.3636363636364,624.0,426.3636363636364,624.0,426.3636363636364
(contents of columns described in link above)
Originally by user75947. Source · Licensed CC BY-SA 4.0
user75947
4y ago
0
Generated from our catalog & community — verify before relying on it.
In GIMP, you can try sharpening and contrast-enhancement to make the bead-like structures easier to see, but keep in mind sharpening does not create new detail—it only emphasizes what is already there.
Useful GIMP options mentioned:
- Filters > Enhance > Sharpen (Unsharp Mask): a standard way to increase apparent sharpness.
- Sharpen tool: manually paint sharpening onto the specific areas you need.
- Filters > Enhance > Wavelet Decompose: in GIMP 2.10, duplicating the finer-scale layers (such as Scale 1 and Scale 2) can boost fine detail.
- Edge detection: can help highlight boundaries between adjacent structures.
- Increase contrast: sometimes this helps more than sharpening for identifying features.
For measurement, a practical workflow is to mark points along a chain with the Path tool and, if needed, export path coordinates to CSV using a path-export script. That can make repeated measurements more consistent.
Because this is scientific analysis, apply the same processing consistently across all images and avoid over-sharpening, which can create misleading edges.
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