Chu Spaces and Channel Theory are well established areas of investigation in the general context of category theory. We review a range of examples and applications of these methods in logic and computer science, including Formal Concept Analysis, distributed systems and ontology development. We then employ these methods to describe human object perception, beginning with the construction of uncategorized object files and proceeding through categorization, individual object identification and the tracking of object identity through time. We investigate the relationship between abstraction and mereological categorization, particularly as these affect object identity tracking. This we accomplish in terms of information flow that is semantically structured in terms of local logics, while at the same time this framework also provides an inferential mechanism towards identification and perception. We show how a mereotopology naturally emerges from the representation of classifications by simplicial complexes, and briefly explore the emergence of geometric relations and interactions between objects.The first part of the paper addresses the initial aim of the tool assembly. We begin by defining and reviewing some of the basic properties of Chu spaces in §2. Although Chu spaces have been traditionally applied to fields such as those listed above, they also have a number of other significant applications of interest here. How Chu spaces can be implemented within Formal Concept Analysis and Domain Theory (e.g. to represent information systems and approximable concepts following Hitzler and Zhang (2004); Krötzsch, Hitzler and Zhang (2005); Scott (1982); Zhang and Shen (2006)) is reviewed in §3. In §4 we discuss representations of spaces (and representations by spaces), spatial coarse-graining and finite sampling of information (Gratus and Porter, 2006; Sorkin, 1991a); we then review the representation of sampled information by simplicial complexes constructed "above" the sampled space in §5. The following two sections, §6 and §7 establish a similar working account of Channel Theory. We survey a number of motivating examples and applications, including Distributed Systems (The category-theoretic concepts of cocone and colimit (e.g. Awodey (2010)) naturally arise in both Chu space and Channel Theory descriptions; we review these concepts in §8 with illustrative examples.The second part of the paper presents new results. We begin in §9 with brief reviews of perception, categorization and attention as neurocognitive processes and of multi-layer recurrent network models (e.g. Friston (2010); Grossberg (2013)) of these processes. In §10, we re-describe perception and categorization, using the Chu space and Channel Theory tools assembled in the first part, in a way that makes explicit the dualities between dynamic and static properties, individuals and categories, and states and events. We capture these dualities in a "cone-cocone diagram" that formalizes the inferential steps required to link object tokens together to produce a "...