Update README.md

README.md

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 license: mit
 ---
 
-# The manually verified in situ hybridization fluorescence images and point coordinate dataset.
+# FISH_spots Dataset
 
+The manually verified in situ hybridization fluorescence images and point coordinate dataset.
+This dataset contains images and annotations for the task of single-molecule fluorescence in situ hybridization (FISH) spot detection, supporting 2D, 3D, and simulated noisy data. The structure is designed for deep learning model development, training, and evaluation.
+
+## Directory Structure
+```
+FISH_spots/
+├── 2d/
+│ ├── csv/
+│ ├── image/
+│ ├── image_raw/
+│ └── meta.csv
+├── 3d/
+│ ├── csv/
+│ ├── image/
+│ ├── meta_test.csv
+│ └── meta_valid.csv
+└── noise/
+├── csv/
+├── image/
+├── meta.csv
+├── meta_test.csv
+└── meta_valid.csv
+
+```
+
+## Download
 ```bash
 # Make sure you have git-lfs installed (https://git-lfs.com)
 git lfs install
 git clone https://huggingface.co/datasets/GangCaoLab/FISH_spots
 ```
+
+## Data Content and Annotation Format
+
+- **image directory**  
+  Contains 512×512 image patches used for training. The images are ready for use by deep learning models, in standard formats such as PNG or TIFF.
+
+- **csv directory**  
+  Stores CSV files containing annotated spot positions for each corresponding image patch. Each row records the coordinates and other metadata of detected or simulated spots.
+
+- **meta*.csv**  
+  `meta.csv`,  provide global metadata.
+
+## 2D Dataset
+
+- Includes data used in the U-FISH publication, comprising both real experimental data and simulated data.
+- Covers 7 different experimental sources, providing diversity (real and simulated conditions).
+- Contains over 4,000 images and 160,000 annotated spot positions.
+- Suitable for benchmarking model generalization and spot detection in varied scenarios.
+
+## 3D Dataset
+
+- Mainly generated via simulation, representing spot distributions under 3D imaging conditions.
+- Provides 3D image patches and coordinate-based annotations.
+- Includes `meta_test.csv` and `meta_valid.csv` for easy split management.
+
+## Noise Dataset
+
+- Contains simulated noisy images aimed at testing model robustness to noise.
+- Structure mirrors the 3D dataset, with patches, annotations, and metadata files.
+
+## Citation
+
+If you use this dataset in your research, please cite the U-FISH paper.