Description
Subtract log10(intensity-darkOffset) from log10(referenceIntensity-darkOffset).
Stain analysis distinguishes measured intensity, blank correction, optical density, and linear channel coordinates. These are different representations whose interpretation depends on calibration and the supplied stain model.
Subtract log10(intensity-darkOffset) from log10(referenceIntensity-darkOffset).
When to use this tool
Use Stain Channel Optical Density when you need one explicit stain-signal component.
How to use the tool and how it works
- Enter intensity, referenceIntensity, darkOffset. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read opticalDensity. Use the output convention below.
Require intensity and referenceIntensity above darkOffset. Subtract log10(intensity-darkOffset) from log10(referenceIntensity-darkOffset).1
| Input field | Meaning and units | Accepted input |
|---|---|---|
| intensity | Intensity | Required. Finite number. |
| referenceIntensity | Reference Intensity | Required. Finite number. |
| darkOffset | Dark Offset | Required. Finite number. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| opticalDensity | Optical Density | Required. Finite number. |
{
"input": {
"intensity": 10,
"referenceIntensity": 100,
"darkOffset": 0
},
"output": {
"opticalDensity": 1
}
}Limitations and assumptions
- Intensity quantities share one scale; optical density can be negative when measured intensity exceeds reference, and no stain concentration, calibration, or diagnostic meaning is inferred.
- Inputs must satisfy both the field types and the cross-field conditions above. Invalid input causes an error; a successful false flag or documented placeholder is a different result.
- Numeric calculations use binary floating point unless exact decimal-integer arithmetic is explicitly stated. No hidden measurement tolerance or decimal rounding is added; nonfinite or out-of-contract results are rejected. Numeric signed-zero results are exported as zero.
Alternative or Complementary methods
Review the complete imaging and stain calibration, deconvolution model, and appropriate professional interpretation separately.
References
Similar or alternative tools
- Stain Reference Channel Factor
Subtract blank from signal and multiply by nonnegative suppliedReferenceLevel/positive referenceChannel.
- Histology Stain Deconvolution One Channel Term
Return the sum of redOd, greenOd, and blueOd multiplied by their respective supplied coefficients.