EmitoMetrix is an AI-based tool designed to analyze mitochondria from Electron microscopy images, using advanced segmentation and data processing algorithms.

Table of Contents
  1. Installation
  2. Configuration
  3. Example Usage
  4. Use Case
  5. Features
  6. Dependencies
  7. License
  8. Morphometrics Description
  9. Github
  10. More documentation
  11. Our models
  12. Usage
  13. Error Messages
  14. Warning Messages

1 . Installation

Installation instructions are available on the installation page, which includes step-by-step video tutorials.

2 . Usage

After installation:

This tool provides a graphical interface. No command line usage is required.

3 . Configuration

No configuration is needed. The tool is fully functional out of the box. All environments and dependencies are installed automatically.

4 . Use Case

EmitoMetrix is built for researchers, especially in biology and medical fields, who need to process and analyze mitochondrial structures in microscopy images efficiently using AI-powered tools.

5 . Features

6 . Dependencies

No additional software installation is required from the user.

7 . License

This section will be updated based on institutional policy.

8 . Description of Mitochondria morphometrics

9 . Github

For more information and updates, please visit our GitHub repository.

10 . More documentation

For more detailed documentation, please refer to the Usages

11 . Our models

12 . Example Usage

Detailled step

First step

Open Fiji and select the EmitoMetrix plugin from the Plugins menu.

Second step

Choose the input folder containing your folder with images. You should have 2 levels of folders. The first level is the folder with images, and the second level is the images themselves. Exemple : RAWDATA/folderImages/image.tif

Choose the output folder where you want to save the results.

Click on OK

Third step

Choose your computer environment (CPU or GPU) and your system (Windows, Linux, or MacOS). Use Gpu if you have a compatible Nvidia GPU with CUDA installed.

Fourth step

Enter the name of your experiment and select custom.

Fifth step

Choose the general settings for your experiment. You can crop the images and enhance the segmentation for High resolutive images.

Sixth step

Choose the model you want to use for your experiment. You can choose between species-specific or the generalist models.

For each condition, set the MEAN diameter of mitochondria contained in your images. This value is required for segmentation process and must be set in pixels. If needed, set a minimum and/or a maximum value as the diameter of the thickest and largest mitochondria from your images. See the FAQ section for more information about the mitochondria diameter setting.

Seventh step

Click on Ok to start the segmentation process. You have to wait until the process is finished. The time depends on the number of images and the size of the images. You can see the progress in the Fiji console. After the process is finished, you will see a message in the Fiji console. And you have to validate the results by clicking on the validate button.

Eighth step

After the validation, you can see the cellpose mask in the results folder.

Ninth step

After that, the segmentation process is finished. Now you can restart EmitoMetrix plugin to Launch the morphometric analysis. You have to rechoose the input and output folders. they will be the same as before.

Tenth step

The measurement process is finished. You can see the results in the output folder.

Eleventh step

Now you have to restart EmitoMetrix plugin to Launch the data display or data prediction. You have to rechoose the input and output folders. they will be the same as before. if you choose the data display, this generates a report with the results of the morphometric analysis. if you choose the data prediction, this generates a report with the results of the morphometric analysis and the predictive model with a confusion matrix.

ERROR MESSAGE

WARNING MESSAGE