Dynamic Nucleic Acids Lab | Franco Lab · UCLA
Condensate Partition Coefficient Pipeline
View pipeline on GitHub →This pipeline done in python automates the measurements of condensates concentrated within nuclei compared to the surrounding dilute phase using 3D confocal Z-stacks. By processing raw multi-channel fluorescence images through automated segmentation masks, it isolates condensates and nuclei to accurately calculate partition coefficients (PC). This interactive demo showcases a precomputed sample run - reproducing manual ground-truth measurements to within ~6% - and allows you to scroll through individual slices to see and compare the raw channels and segmentation masks.
Interactive Z-Stack Viewer
Scroll through all 55 confocal slices to see, at each depth, the raw channels, the segmentation masks overlaid, and the isolated condensate and nuclei masks.
Headline Result — Sample JABr_2_5_3
The automated pipeline reproduces the manual/Imaris reference partition coefficient to within ~6%.
Raw PC
4.867
Calibrated PC
4.813
Manual reference
≈4.558
Imaris ground truth
Calibrated PC of 4.813 vs. the manual reference of ~4.558 — a deviation of about +5.6%, confirming the automated 3D pipeline agrees with hand-labeled measurements.
Key Metrics
| Metric | Value |
|---|---|
| Construct | JABr |
| Partition coefficient (raw) | 4.867 |
| Partition coefficient (calibrated) | 4.813 |
| Condensate density | 319.46 |
| Dilute density | 65.64 |
| Background | 79.0 |
| Condensates detected | 10 |
| Nuclei detected | 6 |
Precomputed sample run · pipeline not executed live