gpseq_fromfish input

The gpseq_fromfish script allows to add GPSeq-like information (i.e., radial position) to FISH signals retrieved with other tools. Run gpseq_fromfish -h for more details.

Prepare your data

The minimum input comprises:

• A dot coordinates table, with the coordinates to the center of each FISH signal. The table should have at least the following columns:
  • File: integer number corresponding to the image series. This is used to identify the corresponding DNA staining image (expected file name notation: channelName_seriesNumber.tif, e.g., cy5_001.tif).
  • Channel: channel label.
  • x, y, z: dot center coordinates.
• An image directory containing the (possibly deconvolved) DNA staining tiff images. These are used to segment nuclei and characterize the nuclei. If the images where previously segmented, a mask directory can be provided with the -m option.
• An output directory where the output is written to. The folder is created if it does not exists. Running the scripts on the same output folder will overwrite the data (sometimes only partially) without showing any warning, and is thus adviced against.