jeanpat
/ extractParticles.py
Last active
August 29, 2015 13:56
A python function relying on scipy.ndimage to extract region of interest in an image or in a stack of images with a a label image, spurious pixels are removed.
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| def extractParticles(greyIm, LabIm): | |
| locations = nd.find_objects(LabIm) | |
| i=1 | |
| extracted_images=[] | |
| for loc in locations: | |
| lab_image = np.copy(LabIm[loc]) | |
| grey_image = np.copy(greyIm[loc]) | |
| lab_image[lab_image<>i]=0 | |
| grey_image[lab_image <>i]=0 | |
| extracted_images.append(grey_image) |
jeanpat
/ extractParticles.ipynb
Created
January 29, 2014 14:13
Image segmentation can be performed by an image labelling process. Once segmented, it could necessary to isolate in independant images the labelled regions. Think of chromosomes in a metaphase image, if resolving chromosomes overlapps or karyotyping must be performed. The following script takes "two images", (in fact two small numpy arrays:img i…
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jeanpat
/ anisotropy.ipynb
Created
November 27, 2013 10:53
Ipython notebook analysing anisotropy of a segmented object (chromosome image) by successive erosion
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jeanpat
/ anisotropy_RoseDirections.py
Created
November 27, 2013 09:23
This python code implements the morphological "rose des directions" operator, based on morphological erosion. readmagick is used to load an image, another lib could be used.
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| # -*- coding: utf-8 -*- | |
| """ | |
| Created on Thu Apr 7 15:19:19 2011 | |
| @author: Jean-Patrick Pommier | |
| http://www.dip4fish.blogspot.com | |
| """ | |
| from __future__ import division | |
| import numpy as np | |
| from scipy import ndimage as nd |
jeanpat
/ pictures.kv
Created
August 20, 2013 20:10
Interface file for the pictures.py application. Modified version of kivy-example/demo/pictures/pictures.kv
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| #:kivy 1.0 | |
| #:import kivy kivy | |
| #:import win kivy.core.window | |
| FloatLayout: | |
| canvas: | |
| Color: | |
| rgb: 1, 1, 1 | |
| Rectangle: | |
| source: 'data/images/background.jpg' |
jeanpat
/ pictures.py
Created
August 20, 2013 19:52
modified version of kivy-example/demo/pictures/main.py available in kivy package
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| ''' | |
| Pictures demo | |
| ============= | |
| This is a basic picture viewer, using the scatter widget. | |
| ''' | |
| import os | |
| import kivy | |
| kivy.require('1.0.6') |
jeanpat
/ chromoverlapp.ipynb
Created
August 16, 2013 11:52
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jeanpat
/ HMT-SE.ipynb
Created
June 20, 2013 16:18
Several structuring elements used with hit-or-miss operator implemented in mahotas to detect branched-points and end-points
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jeanpat
/ SkeletonToGraph.ipynb
Last active
June 11, 2021 11:05
A ipython notebook. Takes an image, converts its skeleton to a networkx graph
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jeanpat
/ LargestBlob
Created
June 5, 2013 07:29
ipython notebook. Detect the largest blob in an image and calculate its area.
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| { | |
| "metadata": { | |
| "name": "largest object" | |
| }, | |
| "nbformat": 3, | |
| "nbformat_minor": 0, | |
| "worksheets": [ | |
| { | |
| "cells": [ |