Tissue Image Alignment
This module adds a new Tissue Image Alignment image processing function for combining multi-channel images of different staining and imaging cycles. It supports cyclic mIF staining and imaging protocols with integrated co-registration software and provides near pixel-perfect alignment results based on a shared marker in all rounds (e.g. DAPI) for up to ten rounds of imaging.
Tissue Image Alignment
This method enables you to combine multi-channel images of different staining and imaging cycles. One channel needs to be identical in each of the images to be able to do this alignment. The alignment is done in a two-step process, a coarse and then a fine alignment. Note that Docker Desktop needs to be running to use this function.
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Parameter |
Description |
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Reference Channel |
Selects the channel of the reference image that is used for alignment. This channel needs to be present in all the images that should be aligned. |
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Target Channel |
Selects channel of the target image which corresponds to the reference channel and is used for alignment. Depending on the number of inputs set below, you have multiple target images where you have to select the corresponding channel. |
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Maximum Shift in µm |
Defines the maximum allowed translation in µm during the fine alignment. If the maximum is not sufficient, the corresponding tiles are not registered. The default value is 50. Increasing the value leads to longer processing times. |
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Tile Size Setting |
Selects the tiling that is used during processing. |
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– |
Fast |
Uses a bigger tile size for faster alignment. |
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– |
Optimal |
Uses a tile size for optimal balance between speed and accuracy. |
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– |
Accurate |
Uses a smaller tile size for the most accurate alignment. |
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Number of Inputs |
Defines the number of inputs for the method. The minimum number of inputs is two (one reference image and one target image), and you can align up to ten images. For each additional input, a new Target Channel section is displayed above. Additionally, the number of input fields in the Input tool is adapted accordingly. |
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Compress Output File |
Activated: Applies the lossless zstd compression to the output file. Deactivated: Applies no compression to the output file. |
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See also
Combining Multi-Channel Images of Different Staining and Imaging Cycles
With the Tissue Image Alignment you can combine and align up to ten images from different staining and imaging cycles.
- Docker Desktop is running on the PC.
- You have opened the images you want to align. One channel of each image needs to be identical.
- Go to the Processing tab, open the Method tool, and select Tissue Image Alignment.
- The parameters of the function are displayed in the Parameters tool.
- In the Parameters tool, set the Number of Inputs to the number of images you want to combine and align.
- The Target Channel section is updated as well as the number of inputs in the Input tool.
- Open the Input tool and select your Reference Image and every Target Image.
- Your images are selected, and the parameters are updated.
- Go back to the Parameters tool and select the Reference Channel, i.e. the channel of the reference image that is used for alignment.
- You have selected the reference channel.
- For each target image, select the Target Channel that corresponds to the reference channel.
- You have mapped the reference channel to a channel of each target image.
- If necessary, change the other parameters, see Tissue Image Alignment.
- You have set up the alignment.
- At the top of the Processing tab, click Apply.
- The processing starts and all images are aligned and combined into one multi-channel image.