GitHub - Zack4DEV/cellpose_sam_spheres: Cell seeding efficiency measurement using customized Cellpose SAM (cellpose4) models. The goal is to classify cells into four categories and calculate cell properties (number, average brightness, and average area) for each frame

Zack4DEV / cellpose_sam_spheres Public

Notifications You must be signed in to change notification settings
Fork 0
Star 1

Cell seeding efficiency measurement using customized Cellpose SAM (cellpose4) models. The goal is to classify cells into four categories and calculate cell properties (number, average brightness, and average area) for each frame

View license

1 star 0 forks Branches Tags Activity

Star

Notifications

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 9 Commits
data		data
logs		logs
results		results
LICENSE		LICENSE
README.md5		README.md5
cellpose_sam_spheres.ipynb		cellpose_sam_spheres.ipynb
requirements.txt		requirements.txt

Repository files navigation

📊 Cell Seeding Efficiency Measurement with Cellpose + SAM

This project analyzes live cell imaging time-series data using Cellpose, SAM, and Microsam to classify cell states and compute seeding efficiency metrics.

---

📁 Folder Structure

- data/raw/: Original input .tif images
- data/processed/: Segmentations, masks, or extracted features
- results/masks/: Per-frame labeled masks for 4 classes
- results/videos/: AVI visualizations (overlays + masks)
- results/metrics.csv: Table of cell count, area, brightness per frame
- logs/: Daily notes and changelogs

---

🧪 Classification Targets

1. Circular cells (initial frames)
2. Fixed cells (midpoint)
3. Dead circular cells (post-fixation)
4. Fragments or abnormal detections

---

⚙ Workflow

1. Preprocess .tif using Cellpose+SAM
2. Segment and classify per frame
3. Track and extract brightness, area, count
4. Output:
   - Masked videos
   - Combined overlay videos
   - CSV with per-frame stats

---

▶ Output

- metrics.csv: frame, class, avg_brightness, avg_area, count
- AVI videos with overlayed masks and raw frames

---

🧠 Dependencies

Requirements.txt Py packages for the Python environment setup.

---

📆 Logs

Daily logs are maintained in logs/daily.md