https://github.com/im-rises/cells_segmentation
Cells segmentation implemented in MatLab.
https://github.com/im-rises/cells_segmentation
image-processing images matlab matlab-image-processing segmentation
Last synced: 8 days ago
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Cells segmentation implemented in MatLab.
- Host: GitHub
- URL: https://github.com/im-rises/cells_segmentation
- Owner: Im-Rises
- License: mit
- Created: 2022-06-09T01:49:53.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2023-01-07T21:22:15.000Z (about 3 years ago)
- Last Synced: 2025-04-10T01:06:16.048Z (11 months ago)
- Topics: image-processing, images, matlab, matlab-image-processing, segmentation
- Language: MATLAB
- Homepage:
- Size: 142 MB
- Stars: 3
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# cells_segmentation
## Description
Cells segmentation program made in MATLAB.
This program is made for educational purpose.
Analyse group of cells from pictures with image conversion, thresholding, filtering, regions separation and
segmentation.
The goal is to create video with the maximum of cells visible.
## Images
| Original image | Image processed|
|-------------------------------------------------------------------------------------------------------------------------|---|
|  |  |
| Image regions| Image segmentation|
|---|---|
|  |  |
## Videos
A set of videos are available in the video folder. They show the different main step of the image processing.
https://user-images.githubusercontent.com/59691442/174501710-ba668ab4-ab22-4bdb-8adc-d2b0d89f1abd.mp4
https://user-images.githubusercontent.com/59691442/174501630-e911c06d-47a2-416c-b142-b9f2c419df3f.mp4
## Quick start
First thing to do is to have MATLAB, you can find it below:
To run the project, you need to install the MATLAB packages:
- [Image Processing Toolbox](https://fr.mathworks.com/products/image.html)
- [Signal Processing Toolbox](https://fr.mathworks.com/products/signal.html)
- [Image Acquisition Toolbox](https://fr.mathworks.com/products/image-acquisition.html)
Once you have installed everything, you can start the project opening the root folder as a project and starting
the `main.m` script in MATLAB.
## Project architecture
The project is composed of one main script `main.m` that will call all the others script.
The other important scripts are :
- `create_video_from_images.m` to create video from a set of images
- `image_processing.m` to process images
- `image_regions.m` to display regions in a image
- `image_segmentation.m` to segment cells in a image
The three other following files are a set of functions for different way to convert an image to black and white (BW):
- `im2bw_mean` image to BW by using mean
- `im2bw_median` image to BW by using median
- `im2bw_my_version` image by manually changing threshold
**Note**
> You can also use the Otsu's method to convert an image from grayscale to BW.
The `pipe.m` file is to use several functions on one variable
For example, a conversion from grayscale to BW, processing and segmenting image.
To use it there is four example in the code:
```matlab
create_video_from_images(fps, inputFolder, imagesExtension, outputFolder, 'cells-4-bw-processed-segmented.avi', {im2bwSelectedFunc, @image_processing,@image_segmentation});
```
Usage:
```matlab
variable = pipe(variable, {@func1,@func2,@func3});
```
## Documentation
MATLAB:
Datacorner image processing course:
## Authors
Quentin MOREL :
- @Im-Rises
-
[](https://github.com/Im-Rises/cells_segmentation/graphs/contributors)