Imaging system hardware

A method comprising:

• mounting a first substrate comprising a biological sample on a first member of a sample holder such that a first retaining mechanism on the first member retains the first substrate on the first member;
• mounting a second substrate on a second member of the sample holder such that a second retaining mechanism on the second member retains the second substrate on the second member, the second substrate comprising an array of capture probes, wherein a capture probe of the array of capture probes comprises:
• (i) a spatial barcode and (ii) a capture domain;
• adding a reagent solution comprising a permeabilization agent to the first substrate and/or the second substrate;
• operating a first actuator connected to the first member or the second member to adjust a distance between the second member or the first member, respectively, in a direction orthogonal to a surface of the first substrate on which the biological sample is positioned such that the biological sample is in contact with at least a portion of the array of capture probes via the reagent solution, wherein the first actuator is a linear actuator;
• and
• permeabilizing at least a portion of the biological sample via the permeabilization agent of the reagent solution to facilitate transfer of a nucleic acid molecule from the biological sample for capture by the capture probe.