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Add CIMA Lab organization card
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- README.md +77 -5
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README.md
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---
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title:
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---
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title: CIMA Lab
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emoji: 馃敩
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colorFrom: indigo
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license: mit
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short_description: Computational Imaging and Medical AI Lab at CUD, Dubai
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---
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<p align="center">
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<img src="https://raw.githubusercontent.com/cima-lab/.github/main/profile/banner.png" alt="CIMA Lab" width="100%">
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</p>
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<h1 align="center">CIMA Lab</h1>
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<p align="center"><b>Computational Imaging and Medical AI</b></p>
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<p align="center">Canadian University Dubai 路 School of Engineering, Applied Science and Technology</p>
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<p align="center">
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<a href="https://github.com/cima-lab"><img src="https://img.shields.io/badge/GitHub-cima--lab-181717?logo=github&logoColor=white" alt="GitHub"></a>
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<a href="https://www.cud.ac.ae"><img src="https://img.shields.io/badge/Web-cud.ac.ae-0b5fff" alt="Website"></a>
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<a href="mailto:cimalab@gmail.com"><img src="https://img.shields.io/badge/Contact-cimalab%40gmail.com-6f42c1" alt="Email"></a>
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<img src="https://img.shields.io/badge/License-MIT%20by%20default-green" alt="License">
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</p>
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---
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CIMA Lab brings medical imaging, computational biology, clinical AI, and trustworthy AI
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together under one lab at CUD. We host research projects from faculty across schools and
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act as the university's front door for external research collaboration and industry
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engagement.
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This Hugging Face organization is where the lab's **artifacts** live: model checkpoints,
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curated datasets, evaluation reports, and demos. The **code** lives on
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[GitHub](https://github.com/cima-lab). Every model here traces back to a public
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repository and a reproducible environment file.
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## Mission
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Develop, validate, and openly release AI methods for imaging, biology, and health systems.
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Host and connect faculty-led projects. Train researchers at every level. Translate results
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with clinical and industry partners.
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## Research areas
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| # | Area | Focus | Status |
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|---|------|-------|--------|
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| 1 | **Medical and Biological Imaging AI** | Reconstruction, restoration, segmentation, and foundation-model adaptation for radiology, pathology, and microscopy | Founding area |
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| 2 | **Clinical and Health-Systems AI** | Explainable diagnostics, disease progression, health-technology assessment, decision support | Seed projects pending faculty affiliation |
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| 3 | **Computational Biology and Biotech** | Machine learning on omics, protein and molecular data, bio-signal analysis, lab automation | Open call for an area lead |
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| 4 | **Trustworthy and Deployable Health AI** | Explainability, robustness, privacy-preserving and federated learning, regulatory readiness | Cross-cutting, open call for an area lead |
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## Projects
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Volume electron microscopy is our first deep vertical. The four projects below cover the
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full pipeline from raw serial sections to quantified organelles.
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| Project | What it does | Stage | Code | Artifacts |
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|---------|--------------|-------|------|-----------|
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| **MicroSAM LoRA + LLRD** | Parameter-efficient adaptation of the MicroSAM foundation model for mitochondria instance segmentation in EM volumes | Active, checkpoints released | [GitHub](https://github.com/cima-lab/Microsam_llrd) | [microsam-llrd](https://huggingface.co/cimalab-cud/microsam-llrd) |
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| **vEMINR** | Faster isotropic reconstruction for volume EM with implicit neural representations. Published in *Advanced Science* (2026) | Published | [GitHub](https://github.com/cima-lab/vEMINR) | Planned |
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| **vEMstitch** | Fully automatic image stitching for volume EM, in Python and C++ | Maintained | [GitHub](https://github.com/cima-lab/vEMstitch) | Planned |
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| **FlowInpaint** | Inpainting for serial-section images, guided by optical flow from neighbouring sections | Active | [GitHub](https://github.com/cima-lab/FlowInpaint) | Planned |
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## Standards every hosted artifact follows
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- **Permissive license by default.** MIT unless a project needs otherwise.
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- **Traceable.** Every model card names its source commit, training data, and environment lock file.
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- **Reproducible.** Pinned environment and dependency files ship with the code.
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- **Evaluated in the open.** Metrics, the exact split that produced them, and the tuned inference parameters are published together.
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- **No clinical or human-subject data** without ethics approval and a data-use agreement. See [SECURITY.md](https://github.com/cima-lab/.github/blob/main/SECURITY.md).
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## Get involved
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- **Faculty** wanting to affiliate a project: read [GOVERNANCE.md](https://github.com/cima-lab/.github/blob/main/GOVERNANCE.md).
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- **Students:** undergraduate, MSc, and PhD positions are open across all four research areas. Email us.
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- **Partners:** academic, clinical, and industry collaboration is welcome. Read [CONTRIBUTING.md](https://github.com/cima-lab/.github/blob/main/CONTRIBUTING.md).
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## Contact
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[cimalab@gmail.com](mailto:cimalab@gmail.com) 路 [cud.ac.ae](https://www.cud.ac.ae) 路 [github.com/cima-lab](https://github.com/cima-lab)
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