Accompanying dataset for "Inhibitory PD-1 axis maintains high-avidity stem-like CD8+ T cells"

Representative dataset for 3D volumetric imaging of mouse Day 8 tumor-draining inguinal lymph node as shown in Fig. 1 on the manuscript "Inhibitory PD-1 axis maintains high-avidity stem-like CD8+ T cells" (Hor et al., 2025, doi: 10.1038/s41586-025-09440-x). Description: 300µm-thick mouse tumor-draining lymph node sliced with a vibrating blade microtome (Leica VT1200S), immunostained over two iterative cycles (IBEX: Radtke et al., 2020: 10.1073/pnas.2018488117) and optically cleared with Ce3D (Li et al., 2017: 10.1073/pnas.1708981114). Volumetric image was acquired using an inverted Leica Stellaris confocal microscope (Leica) equipped with a pulsed white light laser and four tunable spectral Hybrid Detectors (HyD). Acquisition was performed with a 20x multi-immersion objective (with correction collar adjusted to oil immersion), NA = 0.75 and captured at a digital zoom of 1.5 (0.361µm xy pixel resolution) and 2µm z-step over the full thickness of the tissue slice. Image was acquired at 16 bit depth. Excitation eFluor 450 was performed using a fixed 405nm laser line. Image tiles were taken with 5% overlap and merged using the Leica LAS X Navigator application. The deposited dataset has been converted into Imaris format (.ims) and contains the following channels: OT-I.EGFP, XCR1-venus, TCF-1, SLAMF6, PD-1, BATF, Ki-67. Downstream processing, including segmentation and data extraction, was performed on the NIH Biowulf HPC cluster using a custom distributed processing pipeline available on our Github repository.