Vectorizing a polar coordinate conversion loop in a fingerprint-matching process
You said your code works good, as the input isn't too big, so I won't go ahead an try to vectorize this. So, I've provided a general review of the code.

Overall your code looks nice. You should however attempt to have a bit more spaces

[Tdrow, Tdcol] = size(Td);  &lt;-- This
[Tdrow,Tdcol]=size(Td);     &lt;-- Not this


There are only a few things I would do differently in the code:


You can speed this up quite a bit even without vectorization: The size of the cells Tdp1 and Idp1 are known, so these cells can be pre-allocated in front of the loop:

[Tdp1{1:Tdrow, 1:Idrow}] = zeros(Tdrow, Tdcol);
[Idp1{1:Tdrow, 1:Idrow}] = zeros(Idrow, Idcol);


This way you avoid creating Tdrow*Idrow arrays inside the loop. That should save you some time.
Tdp(:,:) is the same as just Tdp, so you can do:

Tdp1{ii,jj} = Tdp;

Note,  ii and jj are better than i and j as iterator names in Matlab. 
You are converting angles from radians to degrees a few places atan2(x,y) * 180 / pi. Instead, use atan2d(x,y). It returns the value in degrees directly.