# FISHcreation
![logo](assets/FISHcreation.png)
## Overview
FISHcreation is a Python library designed for image processing and analysis, specifically tailored for FISH (Fluorescence In Situ Hybridization) images. The library provides a range of functionalities, from preprocessing TIFF images to merging bounding boxes based on overlap criteria.
## Features
- **Preprocessing**: Functions for reading TIFF images and normalizing them. ([preprocess.py](https://github.com/SimonBon/FISHcreation/blob/main/FISHcreation/src/preprocess.py))
- **Bounding Boxes**: Functions to determine if two bounding boxes should be merged and to merge bounding boxes for a given label. ([process_boxes.py](https://github.com/SimonBon/FISHcreation/blob/main/FISHcreation/src/process_boxes.py))
- **Signal Generation**: Functions to create Gaussian signals and apply them to image patches. ([signals.py](https://github.com/SimonBon/FISHcreation/blob/main/FISHcreation/src/signals.py))
- **Utilities**: Functions to create datasets from bounding boxes. ([utils.py](https://github.com/SimonBon/FISHcreation/blob/main/FISHcreation/src/utils.py))
## Installation
To install the library, you can clone the repository and install the required packages.
```bash
git clone https://github.com/SimonBon/FISHcreation.git
cd FISHcreation
pip install -r requirements.txt
```
or
```bash
pip install FISHcreation
```
## Preprocessing:
```python
from FISHcreation.src import preprocess
image = preprocess.get_cell_background("path/to/image.tiff", normalize=True)
```
## Create FISH images:
```python
fish_patch, boxes, labels = create_FISH(rgb_patch, mask_to_patch, num_red=2, num_green=8)
```
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"description": "# FISHcreation\n\n![logo](assets/FISHcreation.png)\n\n## Overview\n\nFISHcreation is a Python library designed for image processing and analysis, specifically tailored for FISH (Fluorescence In Situ Hybridization) images. The library provides a range of functionalities, from preprocessing TIFF images to merging bounding boxes based on overlap criteria.\n\n## Features\n\n- **Preprocessing**: Functions for reading TIFF images and normalizing them. ([preprocess.py](https://github.com/SimonBon/FISHcreation/blob/main/FISHcreation/src/preprocess.py))\n- **Bounding Boxes**: Functions to determine if two bounding boxes should be merged and to merge bounding boxes for a given label. ([process_boxes.py](https://github.com/SimonBon/FISHcreation/blob/main/FISHcreation/src/process_boxes.py))\n- **Signal Generation**: Functions to create Gaussian signals and apply them to image patches. ([signals.py](https://github.com/SimonBon/FISHcreation/blob/main/FISHcreation/src/signals.py))\n- **Utilities**: Functions to create datasets from bounding boxes. ([utils.py](https://github.com/SimonBon/FISHcreation/blob/main/FISHcreation/src/utils.py))\n\n## Installation\n\nTo install the library, you can clone the repository and install the required packages.\n\n```bash\ngit clone https://github.com/SimonBon/FISHcreation.git\ncd FISHcreation\npip install -r requirements.txt\n```\n\nor \n\n```bash\npip install FISHcreation\n```\n\n## Preprocessing:\n\n```python\nfrom FISHcreation.src import preprocess\nimage = preprocess.get_cell_background(\"path/to/image.tiff\", normalize=True)\n```\n\n## Create FISH images:\n\n```python\nfish_patch, boxes, labels = create_FISH(rgb_patch, mask_to_patch, num_red=2, num_green=8)\n```\n",
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