Counting objects is a fundamental but challenging problem. In this paper, we propose diffusion-based, geometry-free, and learning-free methodologies to count the number of objects in images. The main idea is to represent each object by a unique index value regardless of its intensity or size, and to simply count the number of index values. First, we place different vectors, referred to as seed vectors, uniformly throughout the mask image. The mask image has boundary information of the objects to be counted. Secondly, the seeds are diffused using an edge-weighted harmonic variational optimization model within each object. We propose an efficient algorithm based on an operator splitting approach and alternating direction minimization method, and theoretical analysis of this algorithm is given. An optimal solution of the model is obtained when the distributed seeds are completely diffused such that there is a unique intensity within each object, which we refer to as an index. For computational efficiency, we stop the diffusion process before a full convergence, and propose to cluster these diffused index values. We refer to this approach as Counting Objects by Diffused Index (CODI). We explore scalar and multi-dimensional seed vectors. For Scalar seeds, we use Gaussian fitting in histogram to count, while for vector seeds, we exploit a high-dimensional clustering method for the final step of counting via clustering. The proposed method is flexible even if the boundary of the object is not clear nor fully enclosed. We present counting results in various applications such as biological cells, agriculture, concert crowd, and transportation. Some comparisons with existing methods are presented.