jeanpat
/ C8Skeleton_to_graph-01.ipynb
Created
June 12, 2014 08:19
Converting skeleton to graph. A rough ipython notebook. More explanations here: http://dip4fish.blogspot.fr/2014/05/construct-graph-from-skeleton-image-of.html
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
jeanpat
/ Skeleton_to_Graph.ipynb
Last active
August 29, 2015 14:02
Converting skeleton to graph. A rough ipython notebook. More explanations here: http://dip4fish.blogspot.fr/2014/05/construct-graph-from-skeleton-image-of.html
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
jeanpat
/ SkeletonTo graph.ipynb
Created
June 1, 2014 16:48
Ipython notebook: generate some model images (uppercase letters) and build a graph from their skeleton
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
jeanpat
/ FromSkeletonToGraph.ipynb
Last active
August 29, 2015 14:02
A ipython notebook showing how to convert the skeleton of a binary image into a networkw graph
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
jeanpat
/ C8skel_to_Graph.py
Created
May 30, 2014 21:29
Cell of an ipython notebook containing a function to convert the image of a skeleton defined on a neighborhood of 8 pixels, into a graph (networkx). Depends on numpy, mahotas, networkx
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| import mahotas as mh | |
| import networkx as nx | |
| import numpy as np | |
| def C8skeleton_to_graph(skeletonC8): | |
| #images processing: extraction of branchedpoints, end-points, edges | |
| ep = endPoints(skeletonC8) | |
| bp = branchedPoints(skeletonC8, showSE = False) | |
| ## Label branched-points | |
| l_bp,_ = mh.label(bp) |
jeanpat
/ DrawLetters.py
Created
May 30, 2014 14:48
Draw letters with Pillow using the verdana true type font
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| from PIL import Image, ImageDraw, ImageFont | |
| import mahotas as mh | |
| def makeLetterImage(character, size): | |
| image = Image.new("RGBA", (600,150), (255,255,255)) | |
| draw = ImageDraw.Draw(image) | |
| font = ImageFont.truetype("verdana.ttf", size) | |
| draw.text((5, 0), character, (0,0,0), font=font) | |
| img_resized = np.array(image.resize((300,75), Image.ANTIALIAS)) |
jeanpat
/ MaximalQuadrilateralFromNecklaces.ipynb
Created
April 10, 2014 12:27
Here 4-tuples of points are considered. A necklace is a set of 4-tuples which can be deduced from one to an other one by circular permutations. With four points, when a maximal area quadrilateral is searched it is faster to search it in the set of the six possible necklaces than in the set of the 4!=24 possible permutations of a 4-tuple.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
jeanpat
/ MFISH_colorCombination.ipynb
Created
March 20, 2014 14:41
An ipython notebook showing how to combine five greyscaled images into one RGB MFISH image using scikit-image
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
jeanpat
/ resizeImages.py
Created
February 21, 2014 15:20
Given a list of monochrome images or multispectral images (example rgb, or also a z-stack of images) build a list of images of the same size by adding borders.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| def ResizeImages(ImList): | |
| '''Find the largest width and height of images belonging to a list. | |
| Return a list of images of same width/height | |
| ''' | |
| maxwidth=0 | |
| maxheight=0 | |
| if len(np.shape(ImList[0]))==3: | |
| components = np.shape(ImList[0])[2] | |
| imtype = ImList[0].dtype | |
| for i in range(len(ImList)): |
jeanpat
/ chromosomes extraction from mfish image.ipynb
Last active
August 29, 2015 13:56
This ipython notebook shows how to extract, with scipy.ndimage, chromosomes from a set of mfish images.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.