skills.rest
nahisaho
nahisahoCOMMUNITY
Explore all skills by this author →
GitHub

scientific-image-analysis

Automates microscopy image segmentation, morphometric measurement, and texture analysis via Python libraries.

3|1|Updated Feb 11, 2026
Search Tags:#python#segmentation#microscopy#image-analysis#multichannel#texture#morphometry
One-click install
npx skills add https://github.com/nahisaho/satori --skill scientific-image-analysis
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: scientific-image-analysis
Source: https://github.com/nahisaho/satori/tree/main/src/.github/skills/scientific-image-analysis
Command: npx skills add https://github.com/nahisaho/satori --skill scientific-image-analysis

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Quantitative analysis of optical images is often manual, time-consuming, and prone to inconsistency. This skill automates the core workflow for microscopy image analysis, enabling reliable segmentation, morphometric measurements, and texture analysis across large image sets.

Core Features & Use Cases

  • Automated segmentation: Otsu thresholding, Watershed, and Felzenszwalb segmentation to separate objects in microscopy images.
  • Morphometric analysis: Compute area, perimeter, equivalent diameter, circularity, aspect ratio, solidity, and eccentricity.
  • Texture and channel analysis: Extract GLCM and LBP texture features, perform intensity profiling, and merge multi-channel fluorescence images for combined visualization.
  • Use Case: Researchers can quantify particle size distributions and morphology across multiple images or experiments, enabling high-throughput analysis.

Quick Start

Apply the image-analysis workflow to your microscopy data to segment, measure, and summarize particle morphometrics.

Frequently Asked Questions about scientific-image-analysis

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I automate microscopy image segmentation and morphometric analysis in Python?▼

Automate microscopy image analysis by applying Otsu, Watershed, or Felzenszwalb segmentation to separate objects, then compute morphometric features like area, perimeter, and circularity using scikit-image and numpy functions.

Can I extract GLCM and LBP texture features from multichannel fluorescence images?▼

Extract GLCM and LBP texture features from multichannel fluorescence images by utilizing the provided modular functions to perform intensity profiling and merge channels for combined visualization and texture quantification.

What is the best way to quantify particle size distributions across multiple SEM or TEM images?▼

Quantify particle size distributions across SEM or TEM images by loading datasets into the automated workflow, segmenting particles, and extracting morphometric measurements to output structured CSV files for high-throughput analysis.

Does this microscopy image analysis workflow require specific Python libraries?▼

This workflow requires Python libraries such as scikit-image, scipy, and numpy to execute its modular functions for image loading, preprocessing, segmentation, and morphometric analysis.

How do I generate CSV reports and PNG visualizations from optical microscopy data?▼

Generate CSV reports and PNG visualizations from optical microscopy data by running the automated analysis pipeline, which processes images and directly outputs morphometric measurements and segmented visual results.

Related Skills

Explore More Data & Analytics Skills→
jaechang-hitsjaechang-hits
298

cellpose-cell-segmentation

Segment cells and nuclei in microscopy images using pre-trained Cellpose models.

Community
Intermediate
yangqiongyangqiong

Statistical Analysis Skill

Perform statistical analyses on datasets using pandas, numpy, scipy, scikit-learn, and seaborn.

Community
Intermediate
syxscottsyxscott
1

morphometric_analysis

Extract 64 semilandmarks from fossil images and export TPS, CSV, Excel, and JSON data.

Community
Advanced
tara-shopostara-shopos
3

image_editing

Edit images via natural language prompts using the editImage tool.

Community
Intermediate