Quantification

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Video Tutorial

Now we will binarize the in situ signal for each gene and quantify the optical area coverage within each nucleus. The output will be a series of CSV files that can be read into RUHi.

Quantification

This option takes individual gene expression images from the nonLinear folder and quantifies their expression into tables saved in the analyzedTables folder.

Run from the nonLinear folder…

├── max
      └── crop
            └── regImages
            ├── composite
            └── nonLinear __<- Drag first channel from this folder***__
                  └── analyzedTables

TO RUN:
- Drag-and-drop your first gene image from the nonLinear folder into FIJI and select Quantification from the menu

WHAT HAPPENS:
- Automatic thresholding will take the provided tail of the image’s cumulative histogram via MaxEntropy
- Manual thresholding allows one to manually select the threshold for each image (useful in cases of autofluorescence)

OUTPUT:

• Quantified tables for RUHi analysis in analyzedTables folder

• Quantified image overlays for quality control in the analyzedImages folder

⟵ Previous: Segmentation Next: Overlays ⟶