Problem: Pixels are shifting after clipping a raster using extract by mask
When running the Extract By Mask tool from the Spatial Analyst Toolbox, the output raster is shifted from the original.
The extent used to specify the output raster is based on the feature class being used to 'clip' the data. This results in a slight misalignment of the output raster, when compared to the input raster.
Solution or Workaround
Use the Environment Settings for the Extract By Mask tool to set the extent of the output.
To set the Extent:
i) Open the Environment Settings by clicking on the Environments button on the tool.
ii) Click on General Settings.
iii) Under the Extent heading, select the input raster as the output extent. This populates the Extent parameter.
Another option is to specify the extent using the feature class that is clipping the raster, and then specify the Snap Raster using the input raster in the dialog box below.
iv) Click OK to exit the Environment Settings dialog box and then click OK to run the tool.