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micro-stitch

Implementation of an innovative tool designed for real-time panoramic imaging in an optical microscopy environment.

https://github.com/fiuner-lica/micro-stitch

Science Score: 75.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ✓
    Institutional organization owner
    Organization fiuner-lica has institutional domain (lica.ingenieria.uner.edu.ar)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.8%) to scientific vocabulary

Keywords

computer-vision microscopy-images opencv python3 qml
Last synced: 6 months ago · JSON representation ·

Repository

Implementation of an innovative tool designed for real-time panoramic imaging in an optical microscopy environment.

Basic Info
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 0
  • Open Issues: 1
  • Releases: 1
Topics
computer-vision microscopy-images opencv python3 qml
Created almost 4 years ago · Last pushed 7 months ago
Metadata Files
Readme License Citation

README.md

Overview

This repository contains the implementation of an innovative tool designed for real-time panoramic imaging in an optical microscopy environment. The tool aims to overcome limitations associated with conventional panoramic image construction techniques, offering an efficient and high-quality solution through the use of computer vision algorithms.

DOI

Motivation

In the field of optical microscopy, analysts commonly rely on a macroscopic reference frame to locate specific details in samples. Often, computational tools are employed to construct high-resolution panoramic images from lower-resolution captures. However, this traditional process is tedious, time-consuming, and often yields low-quality results in terms of image resolution.

Key Features

  • Continuous Image Acquisition: The tool employs an innovative strategy of continuously forming the image while traversing the sample by moving the microscope stage.

  • Panoramic Construction Algorithm: An advanced algorithm based on computer vision tools has been developed for efficient real-time panoramic image construction.

  • Testing and Validation: The repository includes tests conducted in simulated environments and a real optical microscope. Simulated tests have shown promising results, demonstrating the ability to reconstruct images accurately. Tests on the optical microscope have yielded encouraging results in terms of speed and image quality.

  • Identification of Intrinsic Aberrations: Tests on the optical microscope have also allowed the identification of sources of intrinsic instrument aberrations, contributing to improving the technique's robustness.

Compatibility

This project has been tested and is compatible with the following environment:

  • Operating System: Windows
  • Python Version: 3.x

Clonning de repository

1 - Clone the repository

2 - Create a virtual enviroment with: bash python3 -m venv /path/name_venv

3 - Activate venv with (Windows):

.\.name_venv\Scripts\Activate.ps1

4 - Install dependencies

py -m pip install -r requirements.txt

User Interface

The tool features a user-friendly interface built with QML and Qt.

Video demo

Micro Stitch

To launch the tool with the graphical user interface, run:

bash cd micro_stitch python main.py

Contributions and Issues

Contributions are welcome! Please fork the repository and create a pull request. If you encounter any issues, please open a new issue here.

License

This project is licensed under the MIT license - see the LICENSE.md file for details.

Owner

  • Name: Laboratorio de Informática y Computación Aplicada
  • Login: FIUNER-LICA
  • Kind: organization
  • Email: lica@ingenieria.uner.edu.ar
  • Location: Argentina

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Diaz Zamboni"
  given-names: "Javier Eduardo"
  orcid: "https://orcid.org/0000-0003-0778-316X"
- family-names: "Fiotto"
  given-names: "Santiago"
  orcid: ""
title: "micro-stitch"
version: 1.0.0
doi: 10.5281/zenodo.1234
date-released: 2025-02-13
url: "https://github.com/FIUNER-LICA/micro-stitch"

GitHub Events

Total
  • Watch event: 1
  • Push event: 3
  • Pull request event: 3
  • Create event: 1
Last Year
  • Watch event: 1
  • Push event: 3
  • Pull request event: 3
  • Create event: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 3
  • Total pull requests: 4
  • Average time to close issues: 4 months
  • Average time to close pull requests: 1 minute
  • Total issue authors: 2
  • Total pull request authors: 2
  • Average comments per issue: 0.33
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: 1 minute
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • dzjavier (2)
  • jordaninsfran (1)
Pull Request Authors
  • dzjavier (4)
  • FiottoS (2)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

requirements.txt pypi
  • Pillow *
  • PySide6 *
  • PySide6-Addons *
  • PySide6-Essentials *
  • PyWavelets *
  • imageio *
  • networkx *
  • numpy *
  • opencv-python *
  • packaging *
  • pyparsing *
  • scikit-image *
  • scipy *
  • shiboken6 *
  • tifffile *