Pommier jeanpat
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
/ 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
/ 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.
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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.
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| 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
/ 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.
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jeanpat
/ DrawLetters.py
Created
May 30, 2014 14:48
Draw letters with Pillow using the verdana true type font
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| 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
/ 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
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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
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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
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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
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