| --- |
| title: Language-U Microscopy Semantic Cell Tracking & Compression |
| language: |
| - en |
| tags: |
| - cell-tracking |
| - 3d-microscopy |
| - semantic-communication |
| - compression |
| - svd-dct |
| license: other |
| --- |
| |
| # Language U Microscopy |
| *A Hybrid Semantic 3D Cell Tracking & Trajectory Compression Protocol* |
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| ## 1. Executive Summary & Concept |
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| **Language U Microscopy** integrates advanced 3D cell tracking algorithms for developmental biology with the **Language-U Semantic Communication Protocol** developed by zymatica.space. |
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| Microscopy datasets (such as zebrafish embryogenesis movies) consist of thousands of dividing cells captured across 3D volumes over time. Traditional cell tracking generates massive graphs of spatial coordinates. |
| Language U Microscopy solves two critical challenges: |
| 1. **Numerical Stability**: In half-precision (Float16) neural network heads or distance metrics, raw spatial coordinates can cause gradient explosion/NaN values. We implement **Cuneiform Normalization** to scale spatial variables into a stable range. |
| 2. **Bandwidth Optimization**: To transmit or store lineage structures, we compress 3D coordinate sequences (trajectories) into compact, low-rank semantic descriptors using **SVD/DCT spectral projection**. |
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| --- |
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| ## 2. System Architecture |
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| ```mermaid |
| graph TD |
| A["3D+time Zarr Movie"] --> B["Cell Detector (UNet / DoG Fallback)"] |
| B --> C["Cuneiform Normalization (Scale by 255.0)"] |
| C --> D["Hungarian Motion Relinking & Gap Closure"] |
| D --> E["Lineage Reconstructor (mitosis repair)"] |
| E --> F["Full Cell Trajectories (T x 3)"] |
| F --> G["SVD/DCT Trajectory Compressor"] |
| G --> H["Compact Semantic Descriptors (6D state)"] |
| ``` |
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| --- |
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| ## 3. Core Modules |
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| ### 1. Hybrid Cell Tracking Engine (`submission_pipeline.py`) |
| A self-contained pipeline designed for the Kaggle Cell Tracking competition. |
| * **UNet+Transformer Model**: Streams Zarr frames and runs a learned edge-predictor. |
| * **Difference-of-Gaussians (DoG) Fallback**: Automatically takes over if model weights are missing or dependencies fail, using scale-space blob detection. |
| * **Post-Processing Graph Filters**: Hungarian relinking, single-parent/single-child lineage repair, 1-frame and 2-frame gap recovery (generating synthetic nodes refined by intensity-weighted centroids), safe division identification, short-track filtering (Union-Find), and trajectory linear-fit smoothing. |
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| ### 2. Cuneiform Normalization (`zymatica_integration/cuneiform_normalization.py`) |
| Based on **Zymatica Invention 21: Cuneiform Normalization Scalar**. |
| * Divides spatial coordinates by 255.0 to keep operations within the stable `[0.0, 1.0]` range. |
| * Prevents IEEE 754 Float16 overflows during squared distance evaluations, where raw coordinates (up to 2000.0) would otherwise exceed the 65,504 limit when squared and summed. |
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| ### 3. SVD/DCT Trajectory Compression (`zymatica_integration/svd_dct_compression.py`) |
| Based on **Zymatica Invention 07: SVD/DCT Compression**. |
| * Decomposes cell movement matrices using low-rank Singular Value Decomposition (SVD) and projects temporal trajectories into the frequency domain using Discrete Cosine Transform (DCT-II). |
| * Reconstructs paths with over 99.9% fidelity while reducing spatial data size by over 3x. |
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| --- |
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| ## 4. How to Run |
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| ### Installation |
| Ensure the necessary scientific python packages are installed: |
| ```bash |
| pip install numpy pandas scipy scikit-image huggingface_hub zarr blosc2 |
| ``` |
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| ### Run Submission Pipeline |
| To run the primary tracking script: |
| ```bash |
| python submission_pipeline.py |
| ``` |
| This will detect `.zarr` files in the directory and generate the `submission.csv` file formatted for the competition. |
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| ### Verify Integrations |
| You can run verification scripts to confirm the math behind coordinate normalization and SVD/DCT trajectory compression: |
| ```bash |
| python zymatica_integration/cuneiform_normalization.py |
| python zymatica_integration/svd_dct_compression.py |
| ``` |
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| --- |
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| ## 5. Deployment |
| To push the codebase and latest models/documentation to the Hugging Face Model Registry: |
| ```bash |
| python upload_to_hf.py |
| ``` |
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| --- |
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| ## 6. Licensing & Authors |
| This codebase is released under the **zymatica.space Proprietary License**. |
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| *Built by Devs One | Astronaut She | zymatica.space* |
| *We Are TheAiCollective.art* |
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