With the Tissue Image Alignment you can combine and align up to ten images from different staining and imaging cycles.

1. Docker Desktop is running on the PC.
2. You have opened the images you want to align. One channel of each image needs to be identical.

1. Go to the Processing tab, open the Method tool, and select Tissue Image Alignment.
2. The parameters of the function are displayed in the Parameters tool.
2. In the Parameters tool, set the Number of Inputs to the number of images you want to combine and align.
3. The Target Channel section is updated as well as the number of inputs in the Input tool.
3. Open the Input tool and select your Reference Image and every Target Image.
4. Your images are selected, and the parameters are updated.
4. Go back to the Parameters tool and select the Reference Channel, i.e. the channel of the reference image that is used for alignment.
5. You have selected the reference channel.
5. For each target image, select the Target Channel that corresponds to the reference channel.
6. You have mapped the reference channel to a channel of each target image.
6. If necessary, change the other parameters, see Tissue Image Alignment.
7. You have set up the alignment.
7. At the top of the Processing tab, click Apply.
8. The processing starts and all images are aligned and combined into one multi-channel image.