179 questions
0
votes
0
answers
78
views
Tree Crown Extraction in ArcGIS Pro Using Watershed Tool for Segmentation of Individual Trees in Urban Area is Not Producing Accurate Results
I'm struggling with extracting tree crowns in an urban area using ArcGIS Pro and could use some advice. I'm open to try a different platform and methodology as well (I work in python and R). Here's ...
- 1
0
votes
0
answers
46
views
Individual tree segmentation using watershed algorithm with lidR package
i am trying to use the watershed algorithm for individual tree segmentation, an embedded function watershed() in EBImage was recruited. However the function cannot ready my CHM and returns an error ...
1
vote
0
answers
37
views
WaterDetect: Unable to clip with a shapefile and 8gb RAM crashed without it
)
I'm trying to run waterdetect with the shapefile clipping option but it seems it cant browse correctly, It gave me 'NoneType' object has no attribute 'FlushCache' error while bands=loader....
2
votes
1
answer
135
views
Watershed adjustment for broken particles
I analyze images with particles, as e.g.
Particles - raw image:
As visible, some of the particles are broken and the program does not always recognize them correctly, as visible in images with ...
- 21
0
votes
1
answer
166
views
Watershed Algorithm
I try to use the "Watershed" algorithm to segment the skull and tumor.
Here is the my code:
import numpy as np
import matplotlib.pyplot as plt
from skimage import io, filters, color
from ...
2
votes
1
answer
216
views
Detection of too many tiny areas when measuring large particles in binary images
I am moving from ImageJ to Python for doing image processing of images showing particles - either on a bench or falling - and trying to write my first code for 1) opening images of particles, 2) ...
- 25
0
votes
0
answers
53
views
I can't generate watershed stream order by the whitebox package in R
I'm having trouble generating the drain order by the whitebox package in R. Could you help me?
When I run the wbt_strahler_stream_order function, the result is not limited to the drainage networks but ...
0
votes
0
answers
108
views
Watershed Algorithm with manual markers in python
I want to apply watershed algorithm to an image with predefined markers using Opencv package. I have a original image for example "coffee_grains.jpg" and a marker image "coffee_markers....
- 159
-1
votes
1
answer
46
views
I am getting following error while installing pyswmm. "error: package directory 'bin' does not exist"
I am getting following error while installing pyswmm. "error: package directory 'bin' does not exist"
`enter image description here
I tried to install pyswmm but getting error message.
0
votes
2
answers
117
views
How to calculate unnested watersheds in GRASS GIS?
I am running into a few issues using the GRASS GIS module r.accumulate while running it in Python. I use the module to calculate sub watersheds for over 7000 measurement points. Unfortunately, the ...
0
votes
0
answers
577
views
How to improve performance of cell segmentation using watershed algorithm with opencv-python
I have tried to segment cells in H&E-stained histopathological images using Watershed algorithm of opencv-python.
The code I used is totally same as Docs opencv code in link below.
Watershed Code ...
- 23
1
vote
1
answer
222
views
Finding the Interface of two regions of a segmented image
I have a segmented (by watershed) image of two regions that share one boundary. How do I easily find the position of the pixels on the interface? I tried using hints from this answer but could not get ...
- 78
1
vote
0
answers
67
views
How do I differentiate individual objects in an image, when they are clustered together and calculate object size
I'm currently trying to measure the size of woodchips within an image using openCV and a reference object(the coin)
(https://i.sstatic.net/GpdJE.jpg).
It mostly works but when the woodchips are close ...
2
votes
0
answers
511
views
OpenCV watershed on Grayscale image
I am ready to pull my hair out, I have no idea what is going on.
I am performing watershed on an image I have. I have created markers for the watershed. I can apply the watershed on my original, 3 ...
- 21
0
votes
0
answers
260
views
Track water flow based on DEM in Python
I'm developing a program about water flow based on DEM which is in Python. There're many potential depression in such DEM. Each pixel has different water depth value and they'll be tracked according ...
- 1
0
votes
0
answers
541
views
Segmentation of small particles using Watershed and Distance Transform
I’m trying to separate the dust particles in a picture. To do so, I was thinking of using the watershed algorithm (it’s the first time for me using it).
The picture I’m working with is the following:
...
- 43
0
votes
2
answers
891
views
how to mark the labels on image using watershed opencv
As this is the output from the watershed and I want to mark the labels like 1,2,3 etc on the regions identified. I have tried to use cv2.puttext as well by using cv2.boudingrect but the labels are not ...
- 13
0
votes
1
answer
337
views
Using Pysheds on non-square Raster
I am using Pysheds for watershed delineation and displaying potential flow networks. Everything works well (like in the GitHub Readme) as long as the raster (TIFF) is square:
But if I try to use a ...
- 115
0
votes
1
answer
408
views
Incorrect label assignment after watershed segmentation (Python)
I am segmenting some particles using skimage.segmentation.watershed.
This works quite well, and I manage to separate them adecuately (see image).
Image after segmentation.
However, when I use ndi....
0
votes
0
answers
135
views
Why can't I get Watershed Ridge Lines when I use watershed in Matlab?
As mentioned in the title, I need to use watershed for image segmentation. And I follow the instruction provided by https://uk.mathworks.com/help/images/marker-controlled-watershed-segmentation.html ...
- 33
1
vote
0
answers
231
views
Watershed algorithm: Various colors on gray background
I am trying to figure out the most effective way of doing image segmentation without using deep learning with a steep learning curve.
In my efforts I have come across the watershed algorithm which ...
- 163
3
votes
1
answer
5k
views
How to import Skimage to segment an image with watershed?
I'm trying to use Skimage to segment an image with watershed, but I always get this error. Do you have a solution please?
AttributeError: module 'skimage.morphology' has no attribute 'watershed'
...
- 33
0
votes
2
answers
587
views
Get Edges/boundary for overlapping image
I have a mask for a dental x-ray here where all teeth are overlapping with each other. I want to count the number of teeth present in the image for that I want to separate overlapping tooths so I can ...
0
votes
1
answer
2k
views
C++ and OpenCV 4.5.3 - (-215: Assertion failed)
Problem : Watershed algorithm
I started app project, for image processing, using OpenCv 4.5.3 and Swift ( with C++ ). I'm fighting with watershaded alg. for a really long time... And i have no clue ...
- 37
-1
votes
1
answer
57
views
Region growing with the watershed transform error
Hello guys I am new to image processing, I've been trying out this code from adfoucart but I have been receiving this error
https://github.com/adfoucart/image-processing-notebooks/blob/main/V31%20-%...
- 24
2
votes
0
answers
804
views
Detect overlapping circles (spheres) with shadows with OpenCV and Python
I am writing a program with OpenCV that detects circles in the structure pictures. I'm using the Watershed method described here.
There is a problem I faced: 3d structure photo is hardly converted ...
1
vote
0
answers
27
views
Watershed segmentation to define river midline
I need to define the midline of a river in a RGB Landsat image1. I obtained a binary image and the distance from background (riverbed), and tried to define the peaks to use as markers for watershed, ...
0
votes
1
answer
473
views
Is there a better way to get accurate count?
i'm working on this project to get accurate number of fishes in images. However, i've used pixellib but couldn't get accurate result. Is there any package that could just count objects in an image and ...
- 51
0
votes
1
answer
89
views
Region growing with the watershed transform
I am trying out the code by adfoucart for Region growing with the watershed transform but I ran into some errors when identifying the markers for the image.
from skimage.filters import rank,gaussian
...
0
votes
0
answers
228
views
What is the ideal steps in using predicted segmentation masks for watershed post processing?
I am experimenting with object segmentation(round shaped objects that are often occur close together). I have used UNET deep neural network architecture for segmentation and obtained segmentation ...
- 185
0
votes
1
answer
180
views
How to segment a batch of beans for neural network
I'm stuck with a problem where I want to identify different coffee beans in a mix.
I created a neural network which is able to identify different beans individually. But in practice, I want to develop ...
- 1
1
vote
1
answer
553
views
Using watershed in scikit-image
Description
The watershed function produces an unexpected result: It seems not to be able to segment my array even though I expect it to.
My Example
from skimage.segmentation import watershed
import ...
- 13k
1
vote
1
answer
1k
views
Drawing circles around cells after watershed segmentation - openCV/Python
I followed a tutorial on watershed segmentation and used it to segment each red blood cell in an image. I'm new to openCV and I would like to know if it is possible to draw circles around the cells by ...
- 235
1
vote
0
answers
268
views
Watershed algorithm in Python
I am trying to use watershed algorithm to separate overlapping cells.
This is my image, and when I used ImageJ, it works quite well as below:
my image ImageJ result
However, when I used skimage ...
- 11
1
vote
1
answer
2k
views
How can I improve Watershed segmentation of heterogenous structures in Python?
I'm following a simple approach to segment cells (microscopy images) using the Watershed algorithm in Python. I'm happy with the result 90% of the time, but I have two main problems: (i) the markers/...
- 93
2
votes
0
answers
461
views
Extracting gridded (netcdf) climate data for an entire watershed polygon
My goal is to extract precipitation data from the Daymet database (https://daymet.ornl.gov/) for each of my 68 watershed polygons. I was able to use the ncdf4 package to download the data:
...
0
votes
0
answers
369
views
Why is watershed markers not working properly?
I'm currently working on an algorithm for automatic nuclei segmentation described in this* paper. I already preprocess my image and have implemented the FRST, which output (if I'm understanding it ...
1
vote
0
answers
816
views
Extract only the t-shirt from an image and remove all other noise using openCV in Python
I want to extract a t-shirt from an image and remove all other noise. I have been trying to use the Watershed Algorithm in Python (openCV), however I can't seem to filter for only the t-shirt. Am I ...
- 73
2
votes
0
answers
514
views
how to remove skull in brain MRI by using watershed
I'm working on detecting the brain tumor by using python. I need some help for the segmentation process in my code. I want to remove the skull part in the brain MRI. I'm using the watershed algorithm ...
- 21
3
votes
1
answer
644
views
How to watershed two connected circles
There are the two images I am working with:
(Here the images are not the same size, but in my programme they are the same)
After taking the skimage.metrics.structural_similarity() of the two images ...
- 450
2
votes
1
answer
618
views
What is a C++ implementation or analogue of the local peak detector skimage.feature.peak_local_max?
I need to find local peaks on the depth image to generate the markers for a watershed algorithm in C++.
My Python implementation uses skimage.feature.peak_local_max to generate the markers for a ...
- 23
2
votes
1
answer
1k
views
Critical parameter behind skimage's watershed "over-segmentation"
I have the following mask of cell nuclei, and my goal is to segment them. However, using what seems to be a very standard approach,
import numpy as np
import matplotlib.pyplot as plt
import matplotlib....
- 698
1
vote
1
answer
1k
views
Why do watershed function from scikit-image does not work when my seed points are exactly as large as the vessels I want to fill
Ok here is the situation, I want to make a watershed of this binary vessels image.
Binary vessels.
I want to use these colored vessels as seed points for the algorithm.
Seed points
It seems that when ...
- 11
0
votes
0
answers
159
views
Problem in image segmentation using watershed on android
I am developing an application that segments images of wounds using the watershed algorithm. For this, the user draws a line in the internal area of the wound (region of interest) and another ...
4
votes
0
answers
1k
views
Counting Objects in an image using OPENCV and Python
I'm currently in the pursue of counting the number of shrimps in a given image. I'm using this test image:
The code I have used so far is the following:
import cv2
import numpy as np
from matplotlib ...
1
vote
1
answer
319
views
Open CV Watershed not segmenting oval objects properly
Attemping to create a way to process images to count different types of tablets. The following code has been working well for circular objects, however oval shapes are creating issues that I cant find ...
- 11
1
vote
0
answers
140
views
How to extract markers for Watershed via image processing methods?
I'm writing application with OpenCV that should segmentate an image like attached below, using watershed segmentation with markers, without the user manually marking the image.
I've tried to use ...
- 31
1
vote
1
answer
2k
views
Extracting objects after watershed segmentation
I need to segment the seeds in the image below and crop them.
https://i.sstatic.net/ndOkX.jpg
They can be pretty close to each other and sometimes overlap, so I chose to use the watershed algorithm ...
- 63
1
vote
3
answers
5k
views
Skimage watershed and particles size detection
I have the following image. I was able to use watershed to detect all the particles using the code below.
However, now I need to calculate the size of each particles in the figure and if I use the "...
- 133
1
vote
0
answers
352
views
Problem in sorting contours according to contour area size
I am segmenting rocks. To compare the results of segmentation, I :
Find the contours of the binary image of the segmented image
Find the contour area
Sort the area
Find the n largest and compare it ...
- 63