I am working on the topic of brain tumor segmentation. I have used "Bounding Box Method
Using Symmetry" algorithm to find and segment the tumor. Following is the output
As you can see that I have successfully segmented the tumor and now want to implement neural network on it. I know the working and mathematics behind a simple neural network but doesn't know how to train neural network to work on my algorithm. In short, I want to know how to begin neural network training. Any simple code or direction, preferably using Matlab, will be highly appreciable.
Image recognition
The general neural networks are used for image recognition, not for pin pointing details in an image. You may design a neural network to tell your whether or not there is a tumor in the image, but it is not a trivial task for a neural network to tell you where it is located.
If you do decide to let your network determine whether or not a given image contains a tumor, you would need a huge amount of images without tumors as well. The ratio of "images with tumor" and "images without tumor" should be close to the actual ratio observed in the real world. If you defere from this ratio, the network will be proned to false positives - as it learns that a majority of the images should contain tumors.
In your case
If you input a MR image which contains a tumor, and want to receive a segmented tumor image, you should probably have 500*500 input signals and 500*500 output signals - and train the network to create a border around the tumor present in the image.
If you extend you question as to explain why you want to make the neural network behave like this, then there might be someone here at SO that could help you!
Related
I have data-set regarding chocolates. I need to detect whether it has scratches or not. I am planning to detect from Convolution Neural Network using Caffe. But how to define which neural network architecture will suit to my data-set?
Also how to generate heat values when there is any scratches in image?
I have tried detect normal image processing algorithms and it did not work.
Abnormal Image
Normal Image
Based on the little info you provide, the network architecture choice should be the last of your concerns. Also "trying normal image processing algorithms" is quite a vague statement.
A few points to consider
How big is the dataset? Are the chocolate photos taken in a controlled setting where they are always similar to your example photos or are they taken in the wild, i.e. where they could have different lighting conditions, positions, etc.? Is the dataset balanced?
How is the dataset labelled? Is it just a class for the whole image specifying normal vs abnormal? If so, you'd just be doing classification, and one way to potentially just visualise the location of the scratches (if they turn out to be the most prominent feature for the classification) is to use gradient-weighted class activation maps. On the other hand, if your dataset has labelled scratch points over images, then you can directly train your network to output heatmaps.
Once your dataset is properly set up with a training and validation set, you can just start with a baseline simple small convolutional network architecture, and then you can try out different and bigger network architectures like VGG16, ResNet, etc., and check whether they improve performance on your validation set.
I am a newbie in the neural network, in my project I need to implement a neural network that uses image pixels as input and will give screen coordinate value as output. I am having Dataset which I have collected by performing an experiment by many volunteers. In details, I need to give only cropped eye pixel into the neural network for training. the cropped eye is of size 30*30 (approx) after resizing. I have created a dataset of users looking at a different specific point on the screen. Each point is on a specific coordinate and that is known to me. It is basically an implementation of one research paper.
If you can suggest me, how should I process to create the Neural network that it would be a great help?
If you want to use input image as input to neural network, you can use Conventional Neural Network. CNN can gives image as input.
If you want to extract feature from image, you can use MLP neural network.
So here is there setup, I have a set of images (labeled train and test) and I want to train a conv net that tells me whether or not a specific object is within this image.
To do this, I followed the tensorflow tutorial on MNIST, and I train a simple conv net reduced to the area of interest (the object) which are training on image of size 128x128. The architecture is as follows : successively 3 layers consisting of 2 conv layers and 1 max pool down-sampling layers, and one fully connected softmax layers (with two class 0 and 1 whether the object is present or not)
I impleted it using tensorflow, and this works quite well, but since I have enough computing power I was wondering how I could improve the complexity of the classification:
- adding more layers ?
- adding more channel at each layer ? (currently 32,64,128 and 1024 for the fully connected)
- anything else ?
But the most important part is that now I want to detect this same object on larger images (roughle 600x600 whereas the size of the object should be around 100x100).
I was wondering how I could use the previously training "small" network used for small images, in order to pretrained a larger network on the large images ? One option could be to classify the image using a slicing window of size 128x128 and scan the whole image but I would like to try if possible to train a whole network on it.
Any suggestion on how to proceed ? Or an article / ressource tackling this kind of problem ? (I am really new to deep learning so sorry if this is stupid question...)
Thanks !
I suggest that you continue reading on the field overall. Your search keys include CNN, image classification, neural net, AlexNet, GoogleNet, and ResNet. This will return many articles, on-line classes and lectures, and other materials to help you learn about classification with neural nets.
Don't just add layers or filters: the complexity of the topology (net design) must be fitted to the task; a net that's too complex will over-fit the training data. The one you've been using is probably LeNet; the three I cite above are for the ImageNet image classification contest.
Since you are working on images, I would suggest you to use a pretrained image classification network (like VGG, Alexnet etc.)and fine tune this network with your 128x128 image data. In my experience until we have very large data set fine tuned network will give more accuracy and also save training time. After building a good image classifier on your data set you can use any popular algorithm to generate region of proposal from the image. Now take all regions of proposal and pass them to classification network one by one and check weather this network is classifying given region of proposal as positive or negative. If it classifying as positively then most probably your object is present in that region. Otherwise it's not. If there are a lot of region of proposal in which object is present according to classifier then you can use non maximal suppression algorithms to reduce number of positive proposals.
I read some books but still cannot make sure how should I organize the network. For example, I have pgm image with size 120*100， how the input should be like(like a one dimensional array with size 120*100)? and how many nodes should I adapt.
It's typically best to organize your input image as a 2D matrix. The reason is that the layers at the lower levels of the neural networks used in machine perception tasks are typically locally connected. For example, each neuron of the first layer of such a neural net will only process the pixels of a small NxN patch of the input image. This naturally leads to a 2D structure which can be more easily described with 2D matrices.
For a detailed explanation I'll refer you to the DeepFace paper which describes the stat of the art in face recognition systems.
120*100 one dimensional vector is fine. The locations of the pixel values in that vector does not matter, because all nodes are fully connected with the nodes in the next layer anyway. But you must be consistent with their locations between training, validating, and testing.
The most successful approach so far was to go with a convolutional neural network with 2D input, just as #benoitsteiner stated. For a far simpler example I'd refer you to a LeNet-5, a small neural network developed for MNIST hand-written digit recognition. It is used in EBLearn for face recognition with quite good results.
If I've understood correctly, when training neural networks to recognize objects in images it's common to map single pixel to a single input layer node. However, sometimes we might have a large picture with only a small area of interest. For example, if we're training a neural net to recognize traffic signs, we might have images where the traffic sign covers only a small portion of it, while the rest is taken by the road, trees, sky etc. Creating a neural net which tries to find a traffic sign from every position seems extremely expensive.
My question is, are there any specific strategies to handle these sort of situations with neural networks, apart from preprocessing the image?
Thanks.
Using 1 pixel per input node is usually not done. What enters your network is the feature vector and as such you should input actual features, not raw data. Inputing raw data (with all its noise) will not only lead to bad classification but training will take longer than necessary.
In short: preprocessing is unavoidable. You need a more abstract representation of your data. There are hundreds of ways to deal with the problem you're asking. Let me give you some popular approaches.
1) Image proccessing to find regions of interest. When detecting traffic signs a common strategy is to use edge detection (i.e. convolution with some filter), apply some heuristics, use a threshold filter and isolate regions of interest (blobs, strongly connected components etc) which are taken as input to the network.
2) Applying features without any prior knowledge or image processing. Viola/Jones use a specific image representation, from which they can compute features in a very fast way. Their framework has been shown to work in real-time. (I know their original work doesn't state NNs but I applied their features to Multilayer Perceptrons in my thesis, so you can use it with any classifier, really.)
3) Deep Learning.
Learning better representations of the data can be incorporated into the neural network itself. These approaches are amongst the most popular researched atm. Since this is a very large topic, I can only give you some keywords so that you can research it on your own. Autoencoders are networks that learn efficient representations. It is possible to use them with conventional ANNs. Convolutional Neural Networks seem a bit sophisticated at first sight but they are worth checking out. Before the actual classification of a neural network, they have alternating layers of subwindow convolution (edge detection) and resampling. CNNs are currently able to achieve some of the best results in OCR.
In every scenario you have to ask yourself: Am I 1) giving my ANN a representation that has all the data it needs to do the job (a representation that is not too abstract) and 2) keeping too much noise away (and thus staying abstract enough).
We usually dont use fully connected network to deal with image because the number of units in the input layer will be huge. In neural network, we have specific neural network to deal with image which is Convolutional neural network(CNN).
However, CNN plays a role of feature extractor. The encoded feature will finally feed into a fully connected network which act as a classifier. In your case, I dont know how small your object is compare to the full image. But if the interested object is really small, even use CNN, the performance for image classification wont be very good. Then we probably need to use object detection(which used sliding window) to deal with it.
If you want recognize small objects on large sized image, you should use "scanning window".
For "scanning window" you can to apply dimention reducing methods:
DCT (http://en.wikipedia.org/wiki/Discrete_cosine_transform)
PCA (http://en.wikipedia.org/wiki/Principal_component_analysis)