Hello Kevin,
I understand that you have a set of images with particles in random locations and want to train a Convolutional Neural Network to detect the coordinates of particles in your images. You want to pass your images that are stored in a multi-image ‘.tiff’ file to the network and also want to provide correct coordinates data for training.
For reading individual image files as a 4D array object (height x width x channel x numberImages), I would suggest you use the ‘imread’ function and loop through the number of images in your stack and concatenate into a new array along the 4th dimension using the ‘cat’ function. You can use the below code as reference:
XTrain=imread("stackexample.tif",1); %% Creating a new array (XTrain) that is going to be the 4D image array
for i=2:5
XTrain=cat(4,XTrain,imread("stackexample.tif",i)); %%Concatenating each image file in the .tiff stack along the 4th dimension of new array
end
For creating the ground truth data i.e. the coordinates of particles on images you can use the ‘Image Labeler’ app and manually mark the coordinates on each image.
In case you already have your coordinates data in any format, convert it into a categorical column vector containing the labels for each image. You can name it ‘YTrain’.
Now, you can create ‘arrayDatastore’ type objects for both the image data and the label data after which you can combine them as a ‘combinedDatastore’ type object. You can use the below code as reference:
%Creating array datastores
adsXTrain=arrayDatastore(XTrain);
adsYTrain=arrayDatastore(YTrain);
%Combining them into a combined Datastore
cmds=combine(adsXTrain,adsYTrain);
You can now use this ‘combinedDatastore’ object as an input for training using ‘trainNetwork’ function. You can set your own training options and can use ‘imageInputLayer’ with a size of one of your images (60X60X1) as the first layer.
net = trainNetwork(cmds,layers,options);
1.You can refer to the following documentation to understand more about reading data from ‘tiff’ files:
2.You can refer to the following documentation to understand more about ‘cat function:
3.Documentation about Image Labeler App:
4.You can refer to the following documentation to understand about inputs to ‘trainNetwork’ function
Hope this helps you to proceed further.
