21st Dec 2023: Spatial distribution of Fv Fm
We want to check that within each colony, the Fv/Fm value isn't varying by a lot across pixels inside our mask.
I've generated a big image from each plate showing the per-pixel Fv/Fm, using the standard 3-sigma masking approach. All pixels outside the mask (background pixels) are just colored white in these images. Images from all plates are shown at the end of this mini write up.
- Overall the value is pretty consistent within a colony - approximately within 0.05 of the colony average
- Sometimes Fv/Fm tends to get larger at the outside of a colony, where intensities are lower
- These images are also good to see the shape of the mask. Sometimes, the mask (and hence the intensities) are smaller around the outside of the plate.
I also computed the standard deviation of the Fv/Fm values for each colony, and then averaged them across all colonies on each plate, resulting in a single number describing the average standard deviation of Fv/Fm within each colony on a single plate.
- In general, the standard deviation of Fv/Fm is 0.01, which I think is very good.
- One plate has a significantly lower average standard deviation, which is 99-M2 (0.05). 99-M1 and 99-M6 are also lower.
Many images now follow, ordered by plate:
