This repository contains a specialized computational pipeline for the 3D morphometric analysis of Cdh2-CRISPR zebrafish embryos. By integrating high-resolution confocal microscopy with automated segmentation and statistical modeling, this tool quantifies the relationship between cell-cell adhesion loss and nuclear architecture.
Does the perturbation of Cadherin-2 (Cdh2)—a critical cell-cell adhesion molecule—lead to predictable changes in nuclear morphometry and spatial packing density?
| 1. 3D Reconstruction | 2. Phenotype Detail |
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| Full 3D volumetric segmentation of the embryonic midline. | Zoomed view of nuclear hypertrophy in Cdh2-CRISPR regions. |
| 3. Segmentation Validation | 4. Spatial Distribution |
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| Overlay of raw confocal data vs. computational labels. | Whole-tissue mapping of the segmented nuclear population. |
- Automated Labeling: Converts raw TIF stacks into unique 3D objects using watershed and thresholding algorithms.
- Validation: High-fidelity overlap between raw fluorescence intensity and computational masks.
- Morphometry: Extraction of 3D Centroids, Volumetric Data (voxels), and Sphericity.
- Real-time Filtering: Dynamic Z-slice depth isolation to study specific tissue layers (e.g., Notochord vs. Neural Tube).
- Statistical Modeling: Automated calculation of Nearest Neighbor Distance (NND) to quantify tissue packing.
- Correlation Analysis: Identified a strong positive correlation (r = 0.61) between nuclear volume and tissue sparsity.
Analysis of the S-BIAD1405 dataset (BioImage Archive) demonstrates that cdh2 deficiency triggers significant nuclear hypertrophy (91.9% volume increase). The observed correlation (r = 0.61) suggests that enlarged nuclei are associated with increased inter-nuclear spacing, indicating a breakdown in the mechanical tension and cohesive packing of the embryonic tissue.
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Clone the repository:
git clone https://github.com/YASH4-HD/Zebrafish-3D-Morphometry-Suite-yash.git cd Zebrafish-3D-Morphometry-Suite-yash -
Install dependencies: pip install -r requirements.txt
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Launch the Dashboard: streamlit run app.py
If you use this suite in your research, please cite it as:
Nama, Y. (2026). Zebrafish-MorphoPro: Quantitative 3D Phenotyping Suite (Version 1.0.0). GitHub. https://github.com/YASH4-HD/Zebrafish-3D-Morphometry-Suite-yash
Yashwant Nama
PhD Applicant | Molecular Biologist & Computational Researcher
Focus: Quantitative Developmental Biology, Mechanobiology, and Reproducible Bioinformatics.
🔗 Connect & Verify:
- ORCID: 0009-0003-3443-4413
- LinkedIn: Yashwant Nama
- Project Website: Streamlit Dashboard