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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