# FISHcreation
## 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)
```
Raw data
{
"_id": null,
"home_page": "https://github.com/SimonBon/FISHcreation",
"name": "FISHcreation",
"maintainer": "",
"docs_url": null,
"requires_python": "",
"maintainer_email": "",
"keywords": "",
"author": "Your Name",
"author_email": "your.email@example.com",
"download_url": "https://files.pythonhosted.org/packages/94/c2/c717856b5d6af6fdea8a6cdf425e2bc9b3bef81f676c69721624e5046b9d/FISHcreation-0.5.tar.gz",
"platform": null,
"description": "# FISHcreation\n\n\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",
"bugtrack_url": null,
"license": "MIT",
"summary": "A brief description of your package",
"version": "0.5",
"project_urls": {
"Homepage": "https://github.com/SimonBon/FISHcreation"
},
"split_keywords": [],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "9da4d3b6db0afc1d98e99c6e9e09b9b49f7f69a71e443e3211afae7933e8e2b4",
"md5": "be92c1edc873291e278d8fff7ef93570",
"sha256": "8ac551e32748c03f7e8de93be7447d3d90f7fb510de367a1b9743a2eb14dc550"
},
"downloads": -1,
"filename": "FISHcreation-0.5-py3-none-any.whl",
"has_sig": false,
"md5_digest": "be92c1edc873291e278d8fff7ef93570",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": null,
"size": 6847,
"upload_time": "2023-11-02T12:20:23",
"upload_time_iso_8601": "2023-11-02T12:20:23.798885Z",
"url": "https://files.pythonhosted.org/packages/9d/a4/d3b6db0afc1d98e99c6e9e09b9b49f7f69a71e443e3211afae7933e8e2b4/FISHcreation-0.5-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "94c2c717856b5d6af6fdea8a6cdf425e2bc9b3bef81f676c69721624e5046b9d",
"md5": "366ac5728e30be3fa4a4a9eadf0b02c2",
"sha256": "f23ba3dc257e45b6c81d7e050277b5d4ef4dca2a023a31532a4389afdae2c876"
},
"downloads": -1,
"filename": "FISHcreation-0.5.tar.gz",
"has_sig": false,
"md5_digest": "366ac5728e30be3fa4a4a9eadf0b02c2",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 5924,
"upload_time": "2023-11-02T12:20:26",
"upload_time_iso_8601": "2023-11-02T12:20:26.377309Z",
"url": "https://files.pythonhosted.org/packages/94/c2/c717856b5d6af6fdea8a6cdf425e2bc9b3bef81f676c69721624e5046b9d/FISHcreation-0.5.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-11-02 12:20:26",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "SimonBon",
"github_project": "FISHcreation",
"travis_ci": false,
"coveralls": false,
"github_actions": false,
"requirements": [],
"lcname": "fishcreation"
}
JSON
