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metadata
title: DNAI
emoji: 🚀
colorFrom: red
colorTo: red
sdk: docker
app_port: 8501
tags:
  - streamlit
pinned: false
short_description: DNA Fiber semantic segmentation for replication assessment
license: mit

DN-AI

This is the official repository for DN-AI, an automated tool for measurement of differentiated DNA replication in fluorescence microscopy images.

DN-AI offers different solutions for biologists to measure DNA replication in fluorescence microscopy images, without requiring programming skills. See the Installation section for instructions on how to install DN-AI.

Features

  • Automated DNA replication measurement: DN-AI can automatically measure the amount of DNA replication in fluorescence microscopy images. We use a deep learning model to segment the images and measure the amount of DNA replication.
  • User-friendly interface: DN-AI provides a web-based user-friendly interface that allows users to easily upload images and view the results. Both jpeg and tiff images are supported.
  • Batch processing: DN-AI can process multiple images at once, making it easy to analyze large datasets. It also supports comparing ratios between different batches of images.

Installation

DN-AI relies on Python. We recommend installing its latest version (3.10 or higher) and using a virtual environment to avoid conflicts with other packages.

Prerequisites

Before installing DN-AI, make sure you have the following prerequisites installed:

Python Package

To install DN-AI as a Python package, you can use pip:

pip install git+https://github.com/ClementPla/DeepFiberQ.git

Graphical User Interface (GUI)

To run the DN-AI graphical user interface, you can use the following command:

DNAI

Make sure you are running this command in the terminal where you have installed DN-AI. This will start a local web server and you will see output similar to:

Then open your web browser and go to http://localhost:8501 to access the DN-AI interface.

Screenshots of the GUI:

DN-AI GUI

Docker

A Docker image is available for DN-AI. You can pull the image from Docker Hub:

docker pull clementpla/dnafiber

Google Colab

We also provide a Google Colab notebook for DN-AI. You can access it here.