For example, to get the eye of the mandrill example image:
image = ExampleData[{"TestImage", "Mandrill"}]
indices = {56, 176};
k = 50;
ImageTake[image, {indices[[1]] - k,
indices[[1]] + k}, {indices[[2]] - k, indices[[2]] + k}]
Indices were obtained by right clicking on the image and choosing "Get Indices".
Regarding how the coordinate system works, the difference between coordinates and indices are that the indice origin is in the top left corner, whereas the coordinate origin is in the bottom left corner.
Update
So in order to use coordinates, we can do this:
ImageTake[
image, {
ImageDimensions[image][[2]],
ImageDimensions[image][[2]]
} - {cor[[2]] + k, cor[[2]] - k}, {cor[[1]] - k,
cor[[1]] + k}]
This code manually transforms the coordinates into indices. But ImageTake says that if the row number is negative, it starts from the bottom. That's exactly how coordinates work, so we can simply do this:
ImageTake[image, -{cor[[2]] + k,
cor[[2]] - k}, {cor[[1]] - k, cor[[1]] + k}]