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What does "cell bin" mean? #118

Open Zhouchlei opened 5 months ago

Zhouchlei commented 5 months ago

I used cellCut cgef to generate cell bin GEF(.cgef) according to common bin GEF and mask file. What is the difference between cell bin and bin 1, bin 100, bin 200? Which "bin" should I choose for downstream analysis?

Clouate commented 5 months ago

Hi, Bin N is a regular N × N(DNBs) square area on the chip. The expression information in the area is the expression information of the Bin N. Note that the DNB points on the rightmost and bottommost sides of the square are not included (except Bin 1). For example, bin 50 uses the expression information of a 50 x 50(DNBs) square area as a basic analysis unit.

You could adjust the values ​​of Bin20, 50, 100, and 200 multiple times according to the cell size of different tissue types and the downstream analysis effect. Among them, Bin20 is similar to the size of animal cells, Bin50 and Bin100 are the Binsize sizes commonly used for analysis, and Bin200 is generally used for fast visualization.

And, Cell Bin is the result of cell segmentation based on microscope images, with the expression information of each cell area as a basic analysis unit.

Zhouchlei commented 5 months ago

Thank you for your reply, which is very helpful to me !