FISHcreation 1.0

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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)
• Bounding Boxes: Functions to determine if two bounding boxes should be merged and to merge bounding boxes for a given label. (process_boxes.py)
• Signal Generation: Functions to create Gaussian signals and apply them to image patches. (signals.py)
• Utilities: Functions to create datasets from bounding boxes. (utils.py)

Installation

To install the library, you can clone the repository and install the required packages.

git clone https://github.com/SimonBon/FISHcreation.git
cd FISHcreation
pip install -r requirements.txt

or

pip install FISHcreation

Preprocessing:

from FISHcreation.src import preprocess
image = preprocess.get_cell_background("path/to/image.tiff", normalize=True)

Create FISH images:

fish_patch, boxes, labels = create_FISH(rgb_patch, mask_to_patch, num_red=2, num_green=8)