Questions tagged [segmentation]

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2
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1answer
61 views

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. ...
2
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0answers
52 views

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 ...
8
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2answers
279 views

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 ...
8
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2answers
177 views

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: ...
2
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0answers
57 views

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 ...
3
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1answer
62 views

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 ...
3
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0answers
61 views

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 ...
5
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0answers
132 views

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 ...
1
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0answers
84 views

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 ...
4
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1answer
167 views

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 ...
4
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1answer
187 views

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 ...
3
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0answers
93 views

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 ...
0
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1answer
117 views

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
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0answers
104 views

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, ...
9
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1answer
427 views

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/...
17
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3answers
853 views

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 ...
10
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2answers
281 views

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 ...
2
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1answer
107 views

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? ...
5
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2answers
144 views

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?...
6
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2answers
280 views

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 ...
15
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4answers
1k views

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 ...
2
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1answer
289 views

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 ...
0
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0answers
50 views

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. ...
2
votes
1answer
82 views

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: ...
2
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1answer
1k views

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 ...
2
votes
1answer
176 views

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 ...
3
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1answer
241 views

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". <...
2
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2answers
189 views

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?
4
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2answers
298 views

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 ...
7
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2answers
725 views

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 ...
2
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0answers
243 views

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. ...
1
vote
1answer
160 views

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 ...
14
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2answers
2k views

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 ...
21
votes
2answers
972 views

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 ...
9
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2answers
1k views

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 ...
2
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1answer
113 views

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: ...
2
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0answers
136 views

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 ...
12
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4answers
834 views

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 ...
20
votes
1answer
517 views

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 ...
21
votes
2answers
752 views

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 ...
53
votes
2answers
4k views

Image segmentation and object separation in 3D using Mathematica

I currently work on an image segmentation scenario to detect cell nuclei in 3D using Mathematica. The data I have are image stacks in the TIFF file format. I would like to keep the sequence of image ...