Image stitching with restricted tile offsets

Stitches images using a modified version of the algorithm described in Globally optimal stitching of tiled 3D microscopic image acquisitions.

The algorithm is modified to include a system to prioritize tile offset values within a distribution values to improve robustness for images containing periodic, or minimal features.

Installation

1. Install Rust
2. Open command line, change working directory to this repository. cd stitching
3. Run cd rust
4. Run cargo install --path .
5. The stitching program is now installed and can be invoked with the stitch command

Basic Usage

Set up a stitch_config.json file in the directory containing your images. The basic format is as follows:

{
  "mode": "3d",
  "overlap_ratio": [0.2, 0.2, 0.2],
  "tiles": [
    {
      "path": "tile1.dcm",
      "x": 0,
      "y": 0,
      "z": 0,
      "width": 100,
      "height": 100,
      "depth": 100
    },
    {
      "path": "tile2.dcm",
      "x": 100,
      "y": 0,
      "z": 0,
      "width": 100,
      "height": 100,
      "depth": 100
    },
    {
      "path": "tile2.dcm",
      "x": 200,
      "y": 0,
      "z": 0,
      "width": 100,
      "height": 100,
      "depth": 100
    }
  ]
}

You can then run stitch <path_to_stitch_config_file> to run stitching. The results will be output in the output folder.

Stitch Config Generator UI

Additionally, you can go to https://webstitch.app/ to easily generate configuration files for both this program and ImageJ.