Prior to encapsulation of Cy5.5, NPs were core-labeled with 10mM Alexa Fluor 488 maleimide (cytometry analysis) or Alexa Fluor 555 maleimide (bulk tissue homogenate analysis) purchased from Thermo Fisher for 4 h in pH 7.4 PBS, then cleaned of free dye by CL-6B size exclusion chromatography and concentrated back to the original concentration (40 mg/mL) using 30kDa spin filters (Millipore). Cy5.5-NPs were synthesized through encapsulation of Cy5.5 dye within the hydrophobic NP polymer core by mixing 5mg/mL Cy5.5 (DMSO) at 10%v/v with 40mg/mL PPS-NP (aqueous), then cleaned of free Cy5.5 dye using three successive 7kDa molecular weight cut-off Zeba spin desalting columns [16 (link)]. The resulting Cy5.5-NPs were injected i.d. into the mouse forelimb.