Slide scanner

P21 heads were fixed in 4% paraformaldehyde solution, dehydrated through an ethanol series, and embedded in methyl methacrylate. The samples were sectioned into 400 µm-thick slices with a precision diamond saw (Isomet 2000, Buehler Ltd). The sections were glued to an acrylic plate with a photolabile acrylate-based adhesive (Technovit 7210 VLC adhesive, Heraeus Kulzer GMBH) before grinding and polishing to a final thickness of ∼200 µm. The sections were subsequently stained with Stevenel׳s Blue and Van Gieson׳s Picro Fuschin, and imaged with a slide scanner (Aperio Technologies).
For histology of P0 heads, frozen sections from Section 2.3 were stained with hematoxylin and eosin, and imaged with a slide scanner (Aperio Technologies).

Embedding, sectioning, and staining of the tissue samples were done at the Veterinary Institute in Harstad, Norway. For each fish, two tissue sections were processed: one sample with lice and one sample without lice excised from a standard area (dorsal part of the fish, under the dorsal fin, and above the lateral line). Tissue samples from the same fish were embedded and sectioned together. The tissue sections were hydrated in water and stained with 1% Alcian blue (Alfa Aesar) in 3% acetic acid for 15 min, transferred to 1% periodic acid (VWR) for 10 min, followed by Schiffs (Sigma-Aldrich^®, Saint-Louis, MO, USA) reagent for 15 min, and finally for 30 s in hematoxylin (VWR, Radnor, PA, USA) before dehydration and mounting. AB/PAS staining stain mucous cells dark blue, purple or pink based on the acidity of the mucins [34 (link)]. AB/PAS-stained tissue sections of Atlantic salmon skin were scanned with an Aperio slide scanner (Leica, Microsystems Nussloch GmbH, Wetzlar, Germany). The digital AI-analysis was performed according to [19 (link)] for the skin tissue samples collected at 21 dpc. In total 36 randomly selected tissue samples (with and without lice), from 18 fish (N = 3 fish per tank) were analyzed with the AI-model.