NIS-Seq Analysis Suite v1.0 - Nuclei Matching
JSB lab 2020-2024

Phenotyping nuclear masks (TIFF, 1 channel, 2048x2048, 16 bit, sorted by tile):


Phenotyping membrane masks (TIFF, 1 channel, 2048x2048, 16 bit, sorted by tile):


In-situ nuclear masks (TIFF, 1 channel, 2048x2048, 16 bit, sorted by tile):


Nuclear alignment file (tab delimited, pheno tile - insitu tile - x - y)


Scaling factor (in-situ pixel size / phenotype pixel size):
Maximum cell movement (in-situ pixels):
Area gating (only pair nuclei with similar size):

Optional: Use overlapping tiles to match nuclei:
Stage positions (time - well - tile - x µm - y µm, with header)
pixel offset per in-situ tile (x):
pixel offset per in-situ tile (y):

Detect, assign, save cells

Inspect raw images:



Type (insitu / phenotype)
Tile
Channel
Brightness
Show spots
Show scaled

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