Questions tagged [segmentation]
The segmentation tag has no usage guidance.
51
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Fast Segmentation
Imagine I have an image of a segmented tissue as follows
what is the fastest way of converting such an image into a mesh-type object in Mathematica? I am familiar with ...
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DSolve is producing a segmentation fault for large systems of equations
The below code runs fine for anything up to a 64^2 matrix. However, moving to 128^2 throws a segmentation fault, which, despite my best efforts to debug, I cannot find a cause for. Or, to be honest, ...
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Rectangular Image Segmentation?
I'd like to segment an image such that the components are rectangles. Is this possible out of the box? For example:
...
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7
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How can I add legends in the ClusteringComponents function?
I am trying to do color separation on this image using ClusteringComponents function (following an example on Wolfram Mathematica webpage). I will like to have a legend identifying each segmented ...
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How to get ComponentMeasurements[] from colorized image?
I'm using a software to segment images. Long story short, the output given is an array of integers (range 0-255), which I show here colorized:
I'm supposing that the software avoids representing two ...
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119
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Separating boundaries from WatershedComponents
I am trying to look for local minimum on the boundaries between watershed regions.
Typically the boundaries are not connected and spanning across the whole image so it is possible to do it through
<...
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0
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176
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How to obtain the adjacency matrix of morphological components?
I am wondering if there's a simple way to obtain the adjacency matrix of the morphological components of a segmented image. Consider the following example (originally, from this question):
...
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2
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How can I find all the rectangles in an image when they overlap?
When I apply MorphologicalComponents to images like the one below (which consist of white rectangles laid on a black background), I get a single object returned, as ...
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175
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Video segmentation
Mathematica v12.1 introduced Video and various functions like VideoFrameMap and ...
- 22k
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82
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Image segmentation on the edge (no pun entended)
I want to detect nuclei from unevenly stained images, which works quite well with LocalAdaptiveBinarize. Unfortunately, in many of these images the imaged area does ...
- 1,354
3
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1
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162
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Segmenting cells from a stained image of cells from microscope
I have an image which has stained cells and I have to segment all the cells.
But the problem is that the cell boundary is not very distinguished where there is staining done because of the stain.
...
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0
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77
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How to segment a 3D data automatically?
I have a data dataCube, which consist of some floating stones and a circular belt. I want to get the 4 biggest stones from the image, and segment out the outer belt ...
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Prevent background segmentation in watershed transform based on marker
I like to reproduce this accepted answer from stackexchange in MMA. While I would like to achieve a better segmentation than what I already got, at the moment my main problem is that the background is ...
- 3,804
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2
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193
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Visualize a string/sequence, emphasizing certain substrings
I need to visualize a sequence, with the ability to emphasize certain segments.
For example, take this sequence seq:
...
- 1,011
2
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0
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73
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Connect the nearest points in segmented image
I am trying computer vision for document analysis of datasheets.And quite new to mathematica
My goal is to connect and segment out the part number with part in the drawing considerably something ...
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1
answer
265
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Reclassify and colorize a grayscale image in several regions according to given pixel value ranges
First of all, my apologies if this is a duplicate question, I did my best at trying to find a previous possible answers.
I’m trying to find a more efficient way to reclass and colorize a single ...
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88
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Always missing one component in Image Segmentation with SelectComponents-WatershedComponents-GradientFilter Method
I hope this is not a too specific issue and it is probably something very simple, but it is driving me insane.
I am trying some image processing on microscopy images to perform cell isolation as ...
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How to efficiently apply PCA followed by SVD to extract the components of PCA?
I am working on segmenting a textured image using Gabor Filters. This is based on this paper. There exist a Matlab implementation of this as well. Earlier I managed to do up to this. With the help of ...
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175
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How to segment a textured image using Gabor Filters?
I am following a matlab implementation of texture segmentation using Gabor filters. My test image (img) is from Brodatz and as ...
- 3,145
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Distinguishing different cars in picture
I recently posted a question. And I got a great answer from Mr. Carl Lange
Image Segmentation
His solution worked like a charm. However, I got another request which is more generic in nature. The ...
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answer
408
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Image Segmentation
I have what should be a pretty simple question for Mathematica gurus. I have a set of images containing cars and a background. I am trying to create a black and white image where the white part is the ...
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125
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How to perform unsupervised texture classification?
Consider a texture mixture (img) from Brodatz.
I want to classify the five different texture patterns and segment the corresponding regions.
Following this,
I ...
- 3,145
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1
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162
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How to segment an image based on MeanEuclideanDistance?
Consider an image (img) as
Now I have partitioned the image using the following command
parts = ImagePartition[img, 32];
...
- 3,145
4
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1
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207
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Highlighting an image with texture segmentation
I'm trying to take an image of a pencil sketch (http://www.vangoghgallery.com/catalog/image/1442/Sower-with-Setting-Sun.jpg) and colorize the different segments based on the texture. So in this image, ...
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Why this simple case of watershed segmentation fails?
(Cross-posted on Wolfram Community)
I tried a simple experiment today with WatershedComponents. I took this image from:
https://fr.mathworks.com/help/images/ref/...
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3
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Image segmentation by pixel value
I'm looking for a way to segment a grayscale image (or a 2D array) by its pixel values. We look at two neighboring pixels, if their values are close within a certain threshold, then we say they are ...
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Is it possible to extract edges shared between two labeled objects?
For the past couple of weeks I have been trying to implement a cell-tracking and lineage mapping algorithm using which biological cells can be tracked in a time-lapse image. The code can be found at ...
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How could a non-convex volume joining the outer points of a 3D anatomical model be created? [duplicate]
I am trying to visualise segmented anatomical models in 3D. Currently, my attemps are very basic, like the following code. What other ways could you come up with? ...
- 3,034
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195
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SoftmaxLayer Incompatible types
Trying to create U-Net similar to this paper from this GitHub project but keep getting "incompatible type" error on the final softmax layer. Any ideas for how to organize data to satisfy Softmax layer?...
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402
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How to get a deformable mesh from this binarized image?
This question is linked to previous question but significantly different:
how to get cell boundaries in the image
I am using Mathematica 10.2. I have a binarized image (see below) and wish to get a ...
- 8,750
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4
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1k
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How to get cell boundaries in the image?
I have a microscope image of some animal tissue and wish to get the contours for all the cells that are present in the image. the cells are connected to the neighbouring cells via these contours. At ...
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370
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Segmentation of different components from a relatively low contrast image
I have a digital image from X-ray tomography as below:
There are three different ingredients/components to be segmented:
the continuous phase, mastics;
the discrete phase I, aggregates;
the ...
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55
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Why is the SelectComponents behaving differently?
based on the code provided by Dr. belisarius at here, I wanted to test it on a single slice of a 3d image. If I write the code in the following way I get the desired output.
...
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88
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MorphologicalPerimeter[] unstable behaviour with increasing threshold values
I have a PET image represented as a list of lists of grey value intensities. Here you can find the file in a "MAT" format (you can import it like: ...
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1
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Is there Sauvola's or Niblack's threshold binarization algorithms?
It seems that there are no Sauvola's or Niblack's built-in algorithms for image binarization.
Maybe someone has ready to use math-code that implement one of these algorithms.
I need one of these ...
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216
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How to complete boundary in masked image?
I am trying to generate a mask of the elliptical boundaries in this object. Any ideas on how I could complete the edge of a partially filled elliptical object? Thus far, I've obtained a mask that is ...
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328
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Problem with ComponentMeasurements and property "Centroid" [closed]
I am showing here three test images to investigate the output of ComponentMeasurements when using the property "Centroid".
<...
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2
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2
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266
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Isolate black square in image
I have the image below and would like to isolate only the black square (on top of it are some brighter rings visible originating from an illumination lamp).
How can that be done?
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4
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2
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349
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Using mask to segment growing cells over multiple timepoints
I am trying to segment some very irregular cells out of images generated by timelapse microscopy. These cells don't fit any simple shape (not circular or elliptical) and they grow and change shape ...
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886
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Finding objects in images with inhomogeneous background
I have the following image where bright circular shaped objects are seen. The image has usually an inhomogeneous background and ...
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2
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0
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377
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How can I analyse and manipulate k-space data of a DICOM imageset? [closed]
I'm very new to Mathematica. I've some MRI images as 3D DICOM data. I want to get the corresponding k-space data to identify all the signals with their corresponding amplitude, frequency and phase. ...
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1
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Data fitted by two linear fits [duplicate]
can anybody help me please and tell me how to fit my set of points by two linear fits? It is always exactly two of them and are always linear and should cover all the data. The second line should ...
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Trainable WEKA segmentation of images
Is there a Mathematica equivalent of Trainable WEKA Segmentation as implemented in Fiji, the image processing software? A Google search did not return any relevant links.
I attach the original image ...
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2
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1k
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Get measurements of touching particles in an image
I have a picture of glass spheres. I want to calculate different properties of these spheres such as circularity, size, and count.
I have managed to fill the white centers of the particles to ...
- 900
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2
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Efficient way to perform local Otsu thresholding on image
I have images of cell nuclei that have locally varying intensity distributions. Therefore, I need a robust local threshold algorithm. LocalAdaptiveBinarize works ...
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139
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RegionBinarize distance parameter has no effect
I'm trying to segment an object from background in noisy micro CT data. The original 3D volume data looks like this:
...
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169
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Draw segment in arrayplot and get intensity value and coordinates in segment
I want to segment an arrayplot donut in to 6 pizza slices and export per segment the coordinates and intensity values of the pixels inside of it.
I found a good example, which used RegionMember to ...
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Segmentation of a microscopy image with uneven illumination
I am trying to do a little image segmentation on some cells taken from microscopy images that have uneven illumination. I am having trouble getting the background of the image cleaned up after ...
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590
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Segmentation of sunspots
I recently went for a walk with my camera and snapped a few pictures of the sun. The pictures didn't turn out too well, but this was to be expected without a telescope. I thought it might be a nice ...
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835
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Object separation from a 2.5D surface
I'm trying to identify the shape and the boundaries of objects. The data was generated with a laser scanner and represent the surface of an area in which many boulders lay on the ground and making up ...
- 441