In this paper we develop a new computational technique called boundary scale-space theory. This technique is based on the topol 1 ogical paradigm consisting of representing a geometric subdivided object K using a one-parameter family of geometric objects { K i } i ≥ 1 all of them having the same number of closed pieces than K.Each piece of K i ( ∀i ≥ 1) presents the same interior part than the corresponding one in K, and a different boundary part depending on the scale i. Working with coefficients in a field, a scale is installed for the algebraic boundary of each piece and a new invariant for cell complex isomorphisms is given in terms of the Betti numbers of the generated boundary-scalespace cell complexes. Moreover, the so called homology boundary scale-space model of K ( hbss -model for short) is introduced here. This model consists of a hierarchical graph whose nodes are the homology generators of the different bound-ary scale levels and whose edges are specified by homology generators of consecutive boundary scale indices linked by ( hbss -transition maps) preserving homology classes. Various codes for each connected subgraph of an hbss -model are defined, which besides being fast and efficient similarity measures for cel-lular structures, they are as well relevant interpretive tools for the hbss -model. Finally, experimentations mainly aimed at clarifying and understanding the notion of hbss -model, as well as conjecturing about new graph isomorphism invariants (seeing graphs as a 1-dimensional cell complexes), are performed.