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Questions tagged [scikit-image]

scikit-image is a Python image processing toolbox for SciPy.

scikit-image is a collection of algorithms for image processing with SciPy. The scikit-image SciKit extends scipy.ndimage to provide a versatile set of image processing routines.

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Extracting patches from 3D image in Python

I'm trying to extract patches from a 3D image as training data for a neural network. But am having trouble reshaping the patches for larger images. I'm currently using view_as_windows, but am open to other methods if they prove more useful. An…
fibbi
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How do I use multiple data points from one Excel column in Python?

I am doing some image processing in python, and need to crop an area of the image. However, my pixel coordinate data is arranged as three values in one excel column seperated by commas, as follows: [1345.83,1738,44.26] (i.e. [x,y,r]) - this is…
CephaloRhod
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How to crop an image using x/y/r pixel coords?

I'm trying to develop some code to crop multiple areas within an image. The only info I have is the x/y pixel coordinates of the top left corner of each crop, and the pixel length of each side (this number is uniform as the crops are all perfect…
CephaloRhod
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How can I detect a 'dark' image border and crop to it using Python (or Perl)?

I have a number of small images that are screen captures from a video. A couple of example images follow (with various typesof edges present): In short, I'm trying to crop the image to the closest part of the 'main' image, which is inside an…
Skeeve
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How to convert an Uploaded JPEG Image to unit8 type in Google Colab/Python?

I am trying to convert an uploaded image(JPEG, gif) into uint8/16 type on Google Colab using skimage.util. # How to Import an image from google.colab import files from IPython.display import Image # Convert to 8-bit uint from skimage.util import…
Soumendra Bagh
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Python/numpy points list to black/white image area

I'm trying to convert a continuous list points (between 0 and 1) into black and white image, representing area under/over list points. plt.plot(points) plt.ylabel('True val') plt.show() print("Points shape-->", points.shape) I can save the image…
Angel Lordan
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Input format for marching_cubes_lewiner()?

This is the first time I am using the marching cubes algorithm and am wondering what would be the right format for volume input for the marching_cubes_lewnier() function? I am following this example and would like to use my set of points in place…
MadPhysicist
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Stitching back label_image arrays from a segmented tiled image

I have an image which has already been tiled and then segmented (outside my pipeline). Segmentation was carried out separately on each tile and I have the corresponding label_image arrays. These are just arrays the same size as the tiles; The value…
Aenaon
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How do draw.ellipsoid and ellipse_stats from sckimage.draw.ellipse work with grid spacing?

I am looking into the https://scikit-image.org/docs/dev/api/skimage.draw.html#skimage.draw.ellipse and skimage.draw.ellipsoid_stats(a, b, c) which claims, I quote Calculates analytical surface area and volume for ellipsoid with semimajor axes…
RMS
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Detecting Malaria Cell in scan image

I use the malaria scan image to classify the image has malaria or not. The data set is downloaded from kaggle. I achieve above 96% of accuracy. Now, I wonder how to detect the cell in the scan image. I need to point out the malaria cell in the image…
user12914245
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Catching Warnings in Function skimage.img_as_uint

I tried both warnings.catch_warnings() and the input parameter force_copy both failed to catch conversion warnings import numpy as np import skimage import warnings mm = np.ones([55,55],dtype=np.float32) with warnings.catch_warnings(): dd =…
paugam
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skimage convert to grayscale resulting to a black image

I am scraping image and trying to convert them into grayscale. But if i view the image. It is plain black. Can someone tell me what is wrong with this? Thanks Here is my snippet import cv2 from skimage import io from skimage import data from…
draw134
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How do I determine how many windows with overlap fit into an array?

The view_as_image function of skimage returns windows of numpy arrays of predetermined size. For example, view_as_windows(array, (20, 96), 5) will return arrays windows of (20, 96) of the original array, sliding 5 rows at a time (if the width of the…
Nicolas Gervais
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scikit-image threshold_multiotsu outputting black frames from video

I'm currently working on a project that takes in a video file, reads individual frames as grayscale, normalizes them, thresholds them, and then outputs them as individual .jpg files. Below I have two functions, frameCapture() and…
Anthony Hackett
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When using sckit-image segmentation and get Process finished with exit code 139 (interrupted by signal 11: SIGSEGV), how do I resolve it

I'm passing a large array (1143, 1252, 365) into skimage.segmentation.slic It kills jupyter notebook kernel, so I am stuck with the code in pycharm and I get: Process finished with exit code 139 (interrupted by signal 11: SIGSEGV) I've tried arrays…
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