This page of our guide Death Stranding explains how to collect Chiral Crystals. The option of collecting crystals is initially unavailable and must be unlocked first.
As a reminder, Chiral Crystals are one of the raw materials in the game. You can encounter them as you travel through the game world. You may find them yourself or by scanning the neighborhood. Unfortunately, the main character can't pick them up at initial stages of the game.
To solve the problem, you need to get a container for crystals - Crystal Collector. This gadget is obtained automatically during the passage of the main story of the game. You need to reach the Distribution Center West of Capital Knot City and, once all things have been completed in that location, start the eighth story quest - Order No. 8 - Collection: Chiral Crystals. This quest consists in collecting the first crystals and you will receive a crystal container for free.
From now on, you can approach the crystals found in the game world and hold down the interaction button to collect them. The game will always tell you how many crystals you managed to collect (example is shown in the attached picture).
You can Recycle crystals in visited allied locations. However, remember that in-game materials are being collected separately for each location. Once you have moved to another location, you will not find any crystals you have recycled on the list.