Using the default options has a few advantages (no unnecessary disk usage, intensity measurements on original data), but has some downsides (no record of the processed images after the analysis is finished unless the user creates screenshots during the pipeline execution). So what options should you use and when?

First, it's important to note that it is best not to store segments in the Result Image Set if you are using the Temporary Document voxel storage option since the objects will be deleted along with the temporary document once the pipeline finishes. Of course, the pipeline can still be used to export some of the segmentation results in one way or another (Excel spreadsheet of segment values, labelled image, or surfaces of the segmented objects), but it makes it very difficult to review the analysis results.

Second, the option to store the segments in the result image set will be unavailable if the voxels are stored as new channels or overwrite the original image.

Finally, storing the segments on the source image set means that any intensity measurement will be unaffected by the image processing unless the voxel storage is a new channel or replaces the original image data. This is important as many voxel operations have a dramatic effect on intensity values. 

So the options become:

• Temporary Document - Source Image set: This is the default option. The original SIS file remains unmodified except for the objects now stored in it, saving hard disk space and allowing the measurement of intensities on unprocessed data. But as mentioned above there is no image record of the intermediate processing steps unless the user collects screen grabs during the analysis.
• New Document/Image Set - Source Image Set: The processed image is stored separately from the original image data but the objects are stored on the original image. This means that a permanent record of the fully processed image is kept (though not the intermediate steps), but the measurements of intensity are still made on the original data. This can be useful if the processed images are needed later (e.g. for further analysis or for visualisation/movie making), but the intensity measurements need to be made on the original data. Storing the images in a new set may be more convenient in terms of file handling (only one file to move/archive), but leads to a significant increase in file size since it will now contain both the original and processed data, along with any segmented objects.
• This option is also very useful if the pipeline isn't used to create objects but simply to improve the esthetics of the image for visualization (e.g. denoising, background correction, masking)
• New Document/Image Set - Result Image Set: As with the previous option, a permanent record of the processed image is made, with the same implications with regards to file handling, but intensity measurements are made on the processed image.
• New Channel - Both the original and processed images are visible simultaneously which can be useful to create comparison animations. Intensity measurements can be made and compared between both the original and processed image. Some analysis that requires both the unprocessed and processed image is possible (e.g. use autofluorescence signal to segment tissue but also use a background-corrected image to segment cells).
• Replace Original - Often not recommended since the original image information is discarded in favor of the processed image. This could make it difficult to interpret the results and reduces the traceability. As with the option to generate new documents or image sets it can be quite useful for pipelines that do not generate objects but simply enhance the image for visualization. Note that since images are typically imported from other formats, it is usually possible to re-import the original image if needed. 
• Extended Channel Selection - Useful for operations where two different versions of the same channel need to be used. For example, a background-corrected version of the image might be useful to segment small features while a version with a wide blur can be used to segment the tissue. Or maybe need the original version of the image for seed detection and a modified version for region growing.