make_binary_image: Convert Image to Binary with Flexible Thresholding
In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis
make_binary_image R Documentation
Convert Image to Binary with Flexible Thresholding
Description
This function converts a color or grayscale image to a binary image using
Gaussian smoothing and a user-specified thresholding method, such as Otsu's method.
Usage
make_binary_image(img, sigma = 0, threshold_method = "otsu")
Arguments
img
An image object. This can be a color or grayscale image loaded
into R using the EBImage package.
sigma
Numeric value specifying the standard deviation for the Gaussian
blur applied to the grayscale image. Higher values result in more smoothing. 0 skips
smoothing. Default is 0.
threshold_method
Character string specifying the thresholding method to use.
Options are "otsu" for Otsu's method or "mean" for mean thresholding. Default is "otsu".
Details
The function first converts the input image to grayscale using the EBImage::channel() function.
If apply_smoothing is TRUE, it applies a Gaussian blur to the grayscale image to reduce noise
and smooth the image using EBImage::gblur(). The selected thresholding method
(Otsu's method or mean thresholding) is then applied to the processed image to
calculate a threshold, which is used to convert the image to a binary format where
the foreground is marked as TRUE and the background as FALSE.
The function includes basic error checking to ensure that the input is a valid image object.
Value
A binary image (logical matrix) where pixels are either TRUE (foreground) or FALSE (background), based on the chosen thresholding method applied to the (optionally smoothed) grayscale version of the input image.
theMILOlab/SPATA2 documentation built on Feb. 8, 2025, 11:41 p.m.
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| make_binary_image | R Documentation |
Convert Image to Binary with Flexible Thresholding
Description
This function converts a color or grayscale image to a binary image using Gaussian smoothing and a user-specified thresholding method, such as Otsu's method.
Usage
make_binary_image(img, sigma = 0, threshold_method = "otsu")
Arguments
img |
An image object. This can be a color or grayscale image loaded
into R using the |
sigma |
Numeric value specifying the standard deviation for the Gaussian
blur applied to the grayscale image. Higher values result in more smoothing. |
threshold_method |
Character string specifying the thresholding method to use.
Options are |
Details
The function first converts the input image to grayscale using the EBImage::channel() function.
If apply_smoothing is TRUE, it applies a Gaussian blur to the grayscale image to reduce noise
and smooth the image using EBImage::gblur(). The selected thresholding method
(Otsu's method or mean thresholding) is then applied to the processed image to
calculate a threshold, which is used to convert the image to a binary format where
the foreground is marked as TRUE and the background as FALSE.
The function includes basic error checking to ensure that the input is a valid image object.
Value
A binary image (logical matrix) where pixels are either TRUE (foreground) or FALSE (background), based on the chosen thresholding method applied to the (optionally smoothed) grayscale version of the input image.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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