Tissue smFISH at different magnifications, either processed with deconwolf
or not.
NOTE: fields 001 and 005 are swapped between publication and data/plots from this repository.
- Voxel size (ZYX)
- 60x: 300x108.3x108.3 nm
- 20x: 300x325x325 nm
- Fluorophore emission lambda: 665 nm
- 60x: deconwolfed and raw
- 20x: deconwolfed and raw
The images from 20x were previously registered on the 60x ones.
Similarly, undilated masks were also initially provided for both magnifications.
- Mask dilation with no overlap
- Nuclear feature analysis and filtering
- DOTTER analysis and dots export
- Using
DoG
approach,center_of_mass
refinement. - Extract
all dots
, 1 M dots, calculating SNR, nSNR, and FWHM. - Corrected SNR (i.e.,
SNR2
column) added by EW. - Re-scale dots intensity (i.e.,
Value
column) based on deconwolfscaling
factor. - Filter by FWHM and nuclei selection
- Using
- Reference dots selection
- Based on dots intensity threshold
- Generated overlays of selected dots
- Comparing different magnifications
- Shift correction between datasets
- Check overlap and percentage of selected dots