Images

Automatic workflow

If you input image files to start SAW count or SAW realign runs, the following image result files will be saved in /outs/image, depending on the QC result and manual adjustments.

File	Discription
*_regist.tif	The panoramic image, having been registered with the raw expression matrix, is from staining layers in TIFF format.
*_tissue_cut.tif	Tissue segmentation result of the registered panoramic image.
*_mask.tif	Cell segmentation result of the registered panoramic image.
*_mask_edm_dis_10.tif	The result of the cell border expanding is based on the cell segmentation image. *_mask.tif. dis_10 represents the expansion of 10 pixels.

For each image file type, we take a microscope image of mouse whole brain as an example to show:

Registered panoramic image

Tissue segementation in purple

Cell segmentation

Adjusted cell segmentation

Without image

If you start SAW count or SAW realign without an image or the QC result being unsuccessful, tissue segmentation will be performed based on the raw expression matrix.

File	Discription
bin1_img_tissue_cut.tif	Tissue segmentation result of the expression data.

Here we take a microscope image of mouse small intestine as an example to show:

Heatmaop of expression matrix

Tissue segementation based on expression data