Stage 4a — Adsorption Diagnostic

Dataset: 2026-08-31 | Dye: Allura Red | Channel: device_1

Goal: determine whether Allura Red dye is adsorbing onto channel surfaces (floor, ceiling, walls) by comparing the six light images acquired before and after each dye concentration step.

Surface passivation context: the stepped-height channel was treated with BSA (bovine serum albumin) prior to imaging to passivate the channel surfaces and suppress non-specific dye adsorption. All surfaces are polymerized polyethylene glycol diacrylate (PEGDA), 3D-printed with a custom resin formulation on a custom printer. This stage checks how effective that passivation is.

Physical principle: adsorbed dye remains on surfaces even after flushing with buffer. A post-dye light image will therefore show reduced intensity compared to the pre-dye baseline (pre-all). Comparing per-section mean pixel values across all six light images reveals whether and how fast adsorption builds up.

Inputs:

2026-08-31_allura_ave_14bit/device_1/light_pre/mean.tif
2026-08-31_allura_ave_14bit/device_1/light_post_0.375/mean.tif
2026-08-31_allura_ave_14bit/device_1/light_post_1.0/mean.tif
2026-08-31_allura_ave_14bit/device_1/light_post_1.5/mean.tif
2026-08-31_allura_ave_14bit/device_1/light_post_2.5/mean.tif
2026-08-31_allura_ave_14bit/device_1/light_post_5.0/mean.tif
2026-08-31_allura_ave_14bit/device_1/dark/mean.tif
channel_rois.json — crop ROI and 8 section ROIs

Decision rule:

RMS fractional drift < 0.5 % → no significant adsorption; use light_pre for all concentrations
RMS fractional drift ≥ 0.5 % → adsorption detected; use matched light references in Stage 7

Analysis

For each section ROI, the dark-subtracted mean green-channel signal is computed in every light image, then normalised to light_pre. A ratio of 1.0 means the surface transmits the same light as the pre-dye baseline; a ratio below 1.0 indicates reduced transmission consistent with adsorbed dye remaining on the channel surfaces after flushing.

Ratio table (normalised to pre-all)

Background colour: white = no change; red = reduced transmission (ratio < 1); blue = increased transmission (ratio > 1). Scale spans ±3 %.

Section	pre-all	post 0.375 mM	post 1.0 mM	post 1.5 mM	post 2.5 mM	post 5.0 mM
30um	1.0000	0.9992	1.0014	0.9998	0.9999	1.0003
40um	1.0000	1.0004	1.0021	1.0007	1.0011	1.0014
50um	1.0000	0.9994	1.0014	1.0004	1.0009	1.0009
70um	1.0000	0.9991	1.0022	1.0003	1.0011	1.0012
90um	1.0000	0.9996	1.0023	1.0011	1.0014	1.0022
120um	1.0000	1.0000	1.0018	1.0004	1.0007	1.0013
150um	1.0000	1.0000	1.0014	1.0004	1.0010	1.0025
200um	1.0000	0.9989	1.0007	0.9990	0.9997	0.9997

Results

Light-drift line plot

Each line is one section ROI; the x-axis progresses from the pre-dye baseline (pre-all) through each post-concentration light image. The red dotted lines mark the ±0.5 % band used as the adsorption threshold. Flat lines near 1.0 indicate successful BSA passivation; downward drift indicates residual adsorbed dye building up with each successive concentration step.

Ratio heatmap

The same data displayed as a matrix (sections × light steps), with values annotated in each cell. Red = ratio < 1.0 (reduced transmission); blue = ratio > 1.0; white = no change. Colour scale centred at 1.0, spans ±3 %.

Conclusion

✅ No significant adsorption detected.
RMS fractional drift = 0.12% (threshold = 0.5%). Use light_pre as the single reference for all concentrations in Stages 5–7.