Finding pairs of images (homologous chromosomes)

[Jean-Patrick Pommier]

Thanks you for the links. 

Regarding the rbm classifier in the following example 
<http://scikit-learn.org/stable/auto_examples/plot_rbm_logistic_classification.html#example-plot-rbm-logistic-classification-py>. 
At first sight I don't understand what is Y array (X array seems to be the 
set of images).


Jean-Patrick

Le mardi 24 février 2015 17:21:10 UTC+1, Jean-Patrick Pommier a écrit :
>
> Dear All,
>
> I am trying to make pairs of images from the following set of images 
> (chromosomes sorted by size after rotation). The idea is to make a feature 
> vector for unsupervised classification (kmeans with 19 clusters)
>
>
> From each chromosome an integral image was calculated:
>
> plt.figure(figsize = (15,15))
> gs1 = gridspec.GridSpec(6,8)
> gs1.update(wspace=0.0, hspace=0.0) # set the spacing between axes. 
> for i in range(38):
>    # i = i + 1 # grid spec indexes from 0
>     ax1 = plt.subplot(gs1[i])
>     plt.axis('off')
>     ax1.set_xticklabels([])
>     ax1.set_yticklabels([])
>     ax1.set_aspect('equal')
>     image = sk.transform.integral_image(reallysorted[i][:,:,2])
>     imshow(image , interpolation='nearest')
>
> Then each integral image was flatten and combined with the others:
>
> Features =[]
>
> for i in range(38):
>     Feat = 
> np.ndarray.flatten(sk.transform.integral_image(reallysorted[i][:,:,2]))
>     Features.append(Feat)
> X = np.asarray(Features)
> print X.shape
>
> The X array contains *38* lines and 9718 features, which is not good. 
> However, I trried to submit these raw features to kmeans classification 
> with sklearn using a direct example 
> <http://scikit-learn.org/stable/modules/neighbors.html> :
>
> from sklearn.neighbors import NearestNeighbors
> nbrs = NearestNeighbors(n_neighbors=*19*, algorithm='ball_tree').fit(X)
> distances, indices = nbrs.kneighbors(X)
> connection = nbrs.kneighbors_graph(X).toarray()
> Ploting the connection graph shows that a chromosomes is similar to more 
> than one ...
>
>    - Do you think that integral images can be used to discriminate the 
>    chromosomes pairs?
>    - If so, how to reduce the number of features to 10~20? (to get a 
>    better discrimination)
>    
> Thanks for your advices.
>
> Jean-Patrick
>
>
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