Output directory where the js, css files are copied to. This will create a js folder and a css folder in the output. It will copy the required js files of the website, such as jquery.js, bootstrap.js, and other files into the output folder.
This tool will generate a template json file that defines the image processing and other viewer preparation steps.
Input json file, or output file of giotto_setup_image.
TIF image(s). Can be a single image or a set of images (following a naming rule). Need to be TIF format. For a set of images, specify as "pos[POSITION].tif" where [POSITION] (spelled as it is) is a universal field for position ID in the file name. This will fill in the decouple_tiff section of the input json file
Integers. The set of position IDs for the [POSITION] field in the filename. Anywhere [POSITION] appears in the file name (for example "pos[POSITION].tif") will be replaced with the actual position IDs. For example "--change-positions 0 1 2 3" will represent the files "pos0.tif", "pos1.tif", "pos2.tif", "pos3.tif".
Integers. The set of channel IDs of the multi-channel TIF image(s) to be processed. For example, channel 0 may be Nissl channel; channel 1 may be the DAPI; channel 2 may be polyA. Then --change-stain-ids 0 1 2.
Offset file. Required of stitching. Will change the "offset" key in "stitch_image" section, "stitch_coord", "stitch_segmentation_roi" sections of the input json file. Example offset file (tab-separated).
Segmentation roi zip file(s). One zip file for one position (or fov). For multiple files, can use the [POSITION] tag. For example, "RoiSet_Pos[POSITION]_real.zip". Inside each zip are a set of roi files (one roi per cell).
Rotation (degrees). One of 90, 180, 270. Will change the "rotate_image" section of the input json file. Note, it will change the "rotate_coord", "rotate_segmentation" sections of the input json file as well.
Scale factor. For example, 2 means that image(s) will be up-scaled 200%. Note, it will change the "scale_coord", "scale_segmentation" sections of the input json file as well.