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license: mit
task_categories:
- image-segmentation
- object-detection
tags:
- yolo
- phytoplankton
- pseudo-nitzschia
- ifcb
- cell-counting
- instance-segmentation
- marine-biology
- ecology
pretty_name: Pseudo-nitzschia Cell Segmentation Dataset
size_categories:
- n<1K
---
# Pseudo-nitzschia Cell Segmentation Dataset
Instance segmentation dataset for counting individual *Pseudo-nitzschia* cells in chain colonies imaged by the Imaging FlowCytobot (IFCB).
## Dataset Description
*Pseudo-nitzschia* is a genus of harmful algal bloom (HAB) forming diatoms. Cells grow in stepped chains, making individual cell counting challenging. This dataset provides polygon annotations of individual cells within chain colonies, enabling automated cell counting via instance segmentation.
Images were collected by **IFCB104** at the Santa Cruz Municipal Wharf, Monterey Bay, California.
## Dataset Structure
```
data/
images/ # 302 grayscale PNG images of Pseudo-nitzschia chains
labels/ # 301 YOLO polygon segmentation label files
train.txt # 180 images
val.txt # 60 images
test.txt # 61 images
instances_default.json # COCO-format annotations (original CVAT export)
```
## Annotation Format
Labels are in **YOLO polygon segmentation** format:
```
class_id x1 y1 x2 y2 x3 y3 ... xn yn
```
- `class_id`: always `0` (single class: `Pseudo_nitzschia_cell`)
- Coordinates are normalized to `[0, 1]`
- Each line represents one cell polygon
- Multiple lines per file = multiple cells in the image
## Class Information
| ID | Name | Description |
|----|------|-------------|
| 0 | `Pseudo_nitzschia_cell` | Individual cell within a chain colony |
## Statistics
- **Total images:** 302
- **Annotated images:** 301 (with at least one cell polygon)
- **Train/Val/Test split:** 180 / 60 / 61
- **Image format:** Grayscale PNG (variable dimensions, typically ~600x50 px)
- **Source instrument:** IFCB104 (Imaging FlowCytobot)
## Usage with YOLO
```yaml
# cell_seg.yaml
path: ./data
train: ../train.txt
val: ../val.txt
test: ../test.txt
nc: 1
names:
0: Pseudo_nitzschia_cell
```
```bash
yolo segment train data=cell_seg.yaml model=yolo11s-seg.pt epochs=100
```
## Source
- **Instrument:** [IFCB104 - Santa Cruz Municipal Wharf](https://ifcb.caloos.org/timeline?dataset=santa-cruz-municipal-wharf)
- **Annotation tool:** CVAT
- **Associated model:** [patcdaniel/pseudo-nitzschia-yolo11s-seg](https://huggingface.co/patcdaniel/pseudo-nitzschia-yolo11s-seg)
## Citation
If you use this dataset, please cite:
```bibtex
@dataset{pseudo_nitzschia_cell_seg,
author = {Daniel, Patrick C.},
title = {Pseudo-nitzschia Cell Segmentation Dataset},
year = {2025},
publisher = {Hugging Face},
url = {https://huggingface.co/datasets/patcdaniel/pseudo-nitzschia-cell-segmentation}
}
```
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