Nuclear Staining (DAPI)¶

Morphology staining performed after signal readout (PRISM imaging or SPRINTseq sequencing). DAPI labels cell nuclei for segmentation and structural context.

Reagents¶

Reagent	Working Conc.	Notes
DAPI	5 μg/ml in PBS	Nuclear DNA intercalator; Ex/Em 358/461 nm

Manual Staining (Off Flow Cell)¶

Wash: PBS, 2 x 2 min.
Stain: Apply DAPI (5 μg/ml in PBS), incubate RT for 10--15 min, protected from light.
Wash: PBS, 2 x 2 min.
Image: DAPI channel (405 nm excitation).

Automated Staining (In Flow Cell)¶

For SPRINTseq workflows using a flow cell and pump system:

Wash (pre-clean): Pump PBS-T (0.05% Tween), flush 2 min to remove residual sequencing reagents.
Stain: Pump DAPI (5 μg/ml in PBS) until Flow Cell is filled. Stop flow. Incubate RT for 15 min.
Wash (post-clean): Pump PBS, flush 2 min.
Image: Full slide scan in DAPI channel.