A self-contained, biological assay apparatus, comprising: a housing; a dispensing platform including a controllably-movable reagent dispensing system, disposed in the housing; a reagent supply component disposed in the housing; a pneumatic manifold removably disposed in the housing in a space shared by the dispensing platform, removably coupled to a fluidic transport layer and a plurality of reservoirs, wherein the fluidic transport layer, the reservoirs, and a test sample to be introduced therein are disposed in the housing in the space separate from the dispensing platform; a pneumatic supply system removably coupled to the pneumatic manifold in the housing in a space separate from the dispensing platform; a control system coupled to at least one of the dispensing platform and the pneumatic supply system, disposed in the housing, wherein the apparatus is configured as a self-contained, fully automated biological assay-performing apparatus, wherein the self-contained apparatus comprises the fluidic transport layer being configured to separate the sample from reagent input reservoirs in a reservoir layer, and wherein the pneumatic supply system is configured to provide pneumatic signals routed through the pneumatic manifold to affect the transport of the test sample and reagents in the fluidic transport layer, and its plurality of reservoirs, and wherein the dispensing platform further comprises: a motion control system operatively coupled to the reagent dispensing system, wherein the reagent dispensing system includes a reagent dispenser component having a distal dispensing end; and a camera connected to the reagent dispensing system having a field of view that includes at least a selected region of interest of the reservoirs, wherein the camera is configured to record information on the sample from an optical source, and to inform the control system of proper sample loading. a housing; a dispensing platform including a controllably-movable reagent dispensing system, disposed in the housing; a reagent supply component disposed in the housing; a pneumatic manifold removably disposed in the housing in a space shared by the dispensing platform, removably coupled to a fluidic transport layer and a plurality of reservoirs, wherein the fluidic transport layer, the reservoirs, and a test sample to be introduced therein are disposed in the housing in the space separate from the dispensing platform; a pneumatic supply system removably coupled to the pneumatic manifold in the housing in a space separate from the dispensing platform; a control system coupled to at least one of the dispensing platform and the pneumatic supply system, disposed in the housing, wherein the apparatus is configured as a self-contained, fully automated biological assay-performing apparatus, wherein the self-contained apparatus comprises the fluidic transport layer being configured to separate the sample from reagent input reservoirs in a reservoir layer, and wherein the pneumatic supply system is configured to provide pneumatic signals routed through the pneumatic manifold to affect the transport of the test sample and reagents in the fluidic transport layer, and its plurality of reservoirs, and wherein the dispensing platform further comprises: a motion control system operatively coupled to the reagent dispensing system, wherein the reagent dispensing system includes a reagent dispenser component having a distal dispensing end; and a camera connected to the reagent dispensing system having a field of view that includes at least a selected region of interest of the reservoirs, a motion control system operatively coupled to the reagent dispensing system, wherein the reagent dispensing system includes a reagent dispenser component having a distal dispensing end; and a camera connected to the reagent dispensing system having a field of view that includes at least a selected region of interest of the reservoirs, wherein the camera is configured to record information on the sample from an optical source, and to inform the control system of proper sample loading.