https://github.com/mathworks/open-microscopy-data-matlab

Access open microscopy data in MATLAB and create reproducible code
https://github.com/mathworks/open-microscopy-data-matlab

open-data open-science

Last synced: 26 days ago
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Access open microscopy data in MATLAB and create reproducible code

• Host: GitHub
• URL: https://github.com/mathworks/open-microscopy-data-matlab
• Owner: mathworks
• License: bsd-2-clause
• Created: 2023-12-05T11:22:34.000Z (about 1 year ago)
• Default Branch: main
• Last Pushed: 2024-04-25T09:30:59.000Z (9 months ago)
• Last Synced: 2024-11-09T06:08:53.478Z (3 months ago)
• Topics: open-data, open-science
• Language: HTML
• Homepage:
• Size: 37.7 MB
• Stars: 2
• Watchers: 5
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE
  • Security: SECURITY.md

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README

        
[![View Open-Microscopy-Data-MATLAB on File Exchange](https://www.mathworks.com/matlabcentral/images/matlab-file-exchange.svg)](https://www.mathworks.com/matlabcentral/fileexchange/156034-open-microscopy-data-matlab)

[![Open in MATLAB Online](https://www.mathworks.com/images/responsive/global/open-in-matlab-online.svg)](https://matlab.mathworks.com/open/github/v1?repo=mathworks/Open-Microscopy-Data-MATLAB&file=OpenBiologyTutorial.mlx)

# Analyse Open Microscopy Data in MATLAB®

A MATLAB Live Script with accompanying 

- [Jupyter® Notebook](https://github.com/mathworks/Open-Microscopy-Data-MATLAB/blob/main/OpenBiologyTutorial.ipynb), 

- [m file](https://github.com/mathworks/Open-Microscopy-Data-MATLAB/blob/9d6ed32395816ae334ac5e917b5d4a0e68ed292d/OpenBiologyTutorialScript.m)and 

- [reproducible code capsule on Code Ocean®](https://doi.org/10.24433/CO.8820386.v1)

to access and analyze Microscopy image data sets from the Image Data Resource database

## Get started

Use this tutorial to get started with freely available microscopy data at [Image Data Resource](https://idr.openmicroscopy.org/) directly from MATLAB.

- No downloads, no installations

- **Open directly in MATLAB Online™** by clicking this [![Open in MATLAB Online](https://www.mathworks.com/images/responsive/global/open-in-matlab-online.svg)](https://matlab.mathworks.com/open/github/v1?repo=mathworks/Open-Microscopy-Data-MATLAB&file=OpenBiologyTutorial.mlx)

- Step-by-step tutorial shows how to

    - Re-use available data. **Access a list of openly available projects** on Open Microscopy

    - **Query and inspect the metadata** associated with these projects using commands directly from MATLAB (RESTful API)

    - Avoid downloads. **Access specific data** from within the database directly and **avoid time-consuming downloads** of large data

    - **Analyze image data** to identify cells

    - Let others run your code and reproduce your results quickly. **Pubish the results on GitHub** and **make them accessible** using Open With MATLAB Online

    - Allow people to cite you! **Generate a DOI®** for your code by linking your GitHub repository to one of several DOI-generating sites.

- **Live Script** contains **easy-to-use menus** for user to click and select different datasets

- Available on [File Exchange](https://www.mathworks.com/matlabcentral/fileexchange/) for directly installing onto your MATLAB path with one click using the [Add-Ons button](https://www.mathworks.com/help/matlab/matlab_env/get-add-ons.html)

- Accompanying **Jupyter notebook** (.ipynb) for use in a Jupyter environment. More information on MATLAB kernel [here](https://www.mathworks.com/products/reference-architectures/jupyter.html)

- Accompanying [**Code Ocean® reproducible capsule** (.m)](https://doi.org/10.24433/CO.8820386.v1) for one-click reproducibility of the code by anyone, including reviewers.

## About the Image Data Resource

The Image Data Resource (IDR) is a public repository of image datasets from published scientific studies, where the community can submit, search and access high-quality bio-image data.

It can be accessed at [https://idr.openmicroscopy.org/](https://idr.openmicroscopy.org/)

**For advanced users** A detailed guide to the Image Data Resource API can be found [here](https://idr.openmicroscopy.org/about/api.html). To access the REST API use the MATLAB [webread](https://www.mathworks.com/help/matlab/ref/webread.html) function

### Required Products

This tutorial uses the following products

- MATLAB

- Image Processing Toolbox ™

This code has been developed and tested using MATLAB 2023b

**Note**

This tutorial works best when delivered by a tutor. It is important to highlight best practices when working with Open Data, publishing Open Code or making research output reproducible