Most sample losses in cryogenic storage are not caused by a freezer failure. They are caused by a label that fell off, a tube that cracked, or a rack that could not be found — all avoidable, and all cheaper to prevent than to explain.
Label before you freeze
Adhesive applied to a cold surface will lift. Label at room temperature, press the label down firmly along its whole length, and let it bond before the tube goes anywhere near the vapour phase. Use a cryo-rated label and a solvent-resistant marker; an ordinary label and an ordinary pen will both surrender, and a tube whose identity is gone is a tube you have lost.
Understand where the tube is actually rated to sit
Polypropylene tubes rated for −196 °C are generally rated for the vapour phase. Immersing a tube in liquid nitrogen lets liquid enter through the threads; when the tube is brought out and warms, that liquid expands violently. This is the mechanism behind cryovials that fail on removal rather than in storage. Store in vapour phase unless the tube and closure are explicitly rated otherwise, and wear a face shield when handling.
External threads, and why they matter
An externally threaded tube keeps the sealing surface away from the sample. On an internally threaded tube the thread passes through the sample space, so sample can sit in the thread and be dragged across the seal every time the cap is turned. For anything precious, external threading is worth the small extra cost.
Equilibrate before opening
Bring a tube to room temperature before opening it. Opening cold pulls moist room air onto a freezing surface, and the condensate that forms goes straight into your sample. Allow the whole vessel to equilibrate, not just the outside.
Build the inventory before you need it
A rack, box and position scheme created on the day the freezer is filled will still make sense in three years. One invented retrospectively will not. Number the boxes, keep the map somewhere that is not only inside the freezer, and record the position at the moment the sample goes in. The most expensive freezer is one nobody can navigate.
Consumables that earn their place
Cardboard boxes are cheap and fine for a working stock, but they soften with repeated frost cycles; polycarbonate boxes last far longer where a rack is opened often. Canes and cane sleeves suit small numbers of tubes in a dewar. Whichever you choose, standardise — a freezer holding four incompatible box formats wastes more space than any of them save.