Provided herein are methods and systems for processing a nucleic acid molecule from a biological particle (e.g., cell). A plurality of partitions (e.g., droplets) may be generated such that partitions of the plurality of partitions each include a biological particle (e.g., cell) comprising the nucleic acid molecule and a particle (e.g., bead). The partitions can be processed (e.g., imaged) to obtain one or more physical and/or optical properties of their respective biological particles. The nucleic acid molecules included in the partitions can be barcoded and sequenced (e.g., using nucleic acid barcode molecules coupled to the particles of the partitions) to generate nucleic acid sequences of the nucleic acid molecules. The nucleic acid sequences can be electronically associated with the one or more optical properties of the biological particles.
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