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:
