A fluidic device holder configured to orient a fluidic device (300, 200) with respect to mutually perpendicular X, Y, and Z-axes, the device holder comprising: a support structure configured to receive a fluidic device (300, 200), the support structure including a base surface that faces in a direction along the Z-axis and is configured to have the fluidic device (300, 200) positioned thereon; a plurality of reference surfaces facing in respective directions along an XY- plane; an alignment assembly comprising an actuator and a movable locator arm that is operatively coupled to the actuator, the locator arm having an engagement end, the actuator moving the locator arm between retracted and biased positions to move the engagement end away from and toward the reference surfaces, wherein the locator arm is configured to hold the fluidic device (300, 200) against the reference surfaces when the locator arm is in the biased position; a removable cover assembly that is operatively coupled to the actuator, the actuator moving the locator arm to the biased position as the cover assembly is mounted over the fluidic device, the actuator moving the locator arm to the retracted position as the cover assembly is demounted from the fluidic device (300, 200), wherein the cover assembly is configured to engage and hold the fluidic device (300, 200) against the base surface, wherein the cover assembly includes a cover housing having housing legs (436, 438) and a bridge portion that joins the housing legs (436, 438), the housing legs (436, 438) extending in a common direction and having a viewing space located therebetween, the viewing space positioned above the base surface. a support structure configured to receive a fluidic device (300, 200), the support structure including a base surface that faces in a direction along the Z-axis and is configured to have the fluidic device (300, 200) positioned thereon; a plurality of reference surfaces facing in respective directions along an XY- plane; an alignment assembly comprising an actuator and a movable locator arm that is operatively coupled to the actuator, the locator arm having an engagement end, the actuator moving the locator arm between retracted and biased positions to move the engagement end away from and toward the reference surfaces, wherein the locator arm is configured to hold the fluidic device (300, 200) against the reference surfaces when the locator arm is in the biased position; a removable cover assembly that is operatively coupled to the actuator, the actuator moving the locator arm to the biased position as the cover assembly is mounted over the fluidic device, the actuator moving the locator arm to the retracted position as the cover assembly is demounted from the fluidic device (300, 200), wherein the cover assembly is configured to engage and hold the fluidic device (300, 200) against the base surface, wherein the cover assembly includes a cover housing having housing legs (436, 438) and a bridge portion that joins the housing legs (436, 438), the housing legs (436, 438) extending in a common direction and having a viewing space located therebetween, the viewing space positioned above the base surface.