Table 3. Channel specification Description of which cell population is expected to be visible in each channel of the provided videos.

VideoID	CH0	CH1	CH2	CH3
Bold indicates the cells that have been tracked. Brackets reports the type of staining used. The prefix a: or b: is used to indicate which is the corresponding tracking file (e.g. for video 04, b:N.(CMTMR) means that the tracks relative to the neutrophils labelled with CMTMR are in 04b.csv). Legend: Bc = B cells, Tc = T cells, Ne = neutrophils, Dc = dendritic cells, NKs= natural killer cells, Mp = macrophages, AF = auto-fluorescence, BG = background, Coll = collagen.
CS001	BG(FR)	Tc(CMTMR)	a:Tc(HIV-GFP)	Coll
CS002	BG(FR)	Tc(CMTMR)	a:Tc(HIV-GFP)	Coll
CS003	BG(FR)	Tc(CMTMR)	a:Tc(HIV-GFP)	Coll
CS004	a:Ne(UBC-CFP), Dc(CD11c YFP)	Vaccine	a:Ne(UBC-CFP), Coll
CS005	a:Ne(UBC-GFP)
CS006	BG(FR)	Tc(CMTMR)	a:Tc(HIV-GFP)	Coll
CS007	a:Ne(UBC-GFP)
CS008	a:Ne(UBC-GFP)
CS009	a:Ne(UBC-GFP)
CS010	a:Ne(UBC-CFP), Dc(CD11c YFP)	Vaccine	a:Ne(UBC-CFP), Coll
CS011	a:Ne(UBC-GFP), BG	BG	Coll, BG
CS012	a:Tc(CFSE)
CS013	a:Ne(UBC-CFP), Dc(CD11c YFP)	Vaccine	a:Ne(UBC-CFP), Coll
CS014	a:Ne(UBC-GFP)	Vaccine	a:Ne(UBC-CFP), Coll
CS015	a:Ne(UBC-CFP), Dc(CD11c YFP), AF	Ne(CMTMR), AF	a:Ne(UBC-CFP), Coll, AF
CS016	a:Ne(UBC-CFP), Dc(CD11c YFP), AF	Ne(CMTMR), AF	a:Ne(UBC-CFP), Coll, AF
CS017	a:Ne(UBC-CFP), Dc(CD11c YFP), AF	Ne(CMTMR), AF	a:Ne(UBC-CFP), Coll, AF
CS018	a:NK(NCR1 GFP), Mp(CD169 Pe)	Mp(Cd169 Pe)	Vaccine	Coll
LTDB001	a:Ne(UBC-CFP), Dc(CD11c YFP)	Vaccine	a:Ne(UBC-CFP), Coll
LTDB002	a:Ne(UBC-CFP), Dc(CD11c YFP)	Vaccine	a:Ne(UBC-CFP), Coll
LTDB003	a:Ne(UBC-CFP), Dc(CD11c YFP)	Vaccine	a:Ne(UBC-CFP), Coll
LTDB004	Ne(UBC-GFP), a:Ne(UBC-CFP), AF	b:Ne(CMTMR), AF	a:Ne(UBC-CFP), Coll, AF
LTDB005	Ne(UBC-GFP), a:Ne(UBC-CFP), AF	b:Ne(CMTMR), AF	a:Ne(UBC-CFP), Coll, AF
LTDB006	a:Ne(UBC-CFP), Dc(CD11c YFP)	Vaccine, BG	a:Ne(UBC-CFP), Coll
LTDB007	b:Ne(UBC-GFP), a:Ne(UBC-CFP), AF	Ne(CMTMR), AF	a:Ne(UBC-CFP), Coll, AF
LTDB008	a:Ne(UBC-CFP), Dc(CD11c YFP)	Vaccine	a:Ne(UBC-CFP), Coll
LTDB009	a:Ne(UBC-CFP), Dc(CD11c YFP)	Vaccine	a:Ne(UBC-CFP), Coll
LTDB010	Ne(UBC-GFP), BG	a:Bc(CTV)
LTDB011	a:Ne(UBC-GFP), BG	Bc(CD19 RFP)
LTDB012	BG(FR)	a:Tc(CMTMR)	b:Tc(HIV-GFP)	Coll
LTDB013	BG(FR)	Tc(CMTMR)	a:Tc(HIV-GFP)	Coll
LTDB014	b:Bc(Bodipy 650)	Tc(H2B-RFP)	Tc(NFAT-GFP)	a:Bc(Ag+ Hoechst33342)
LTDB015	Tc(CMAC)	a:Tc(CFSE)	Tc(CMTMR)	HEV(Meca-633)
LTDB016	a:Ne(UBC-CFP), Dc(CD11c YFP)	Ne(CMTMR), AF	a:Ne(UBC-CFP), Coll, AF
LTDB017	a:Ne(UBC-CFP), Dc(CD11c YFP)	Ne(CMTMR), AF	a:Ne(UBC-CFP), Coll, AF
LTDB018	Dc(CD11c YFP)	a:NK(CMTMR)
LTDB019	a:NK(CTV), Dc(CD11c YFP)	Vaccine	a:NK(CTV)
LTDB020	BG	a:NK(CMTMR)	BG	Coll