When using fluorescence microscopy, especially for in vitro cell cultures it is common to acquire multiple planes to capture the full depth of the sample. In many cases the 3D information is useful and arivis can use it to segment 3D objects and measure volumetric properties. However, in some cases the main advantage of acquiring a stack is to be able to get the whole sample in focus at the optical resolution that allows us to measure the features of interest. In such cases compressing the stack into a single plane can provide all the information that is required while working from much simpler, and smaller datasets. Maximum Intensity Projections (MIPs) are an efficient way to compress such images into a single plane. 

The first point to note is that many acquisition systems are capable of producing these projection images at the time of capture, or at the time of saving, and that if our imaging device is capable of doing this automatically this may be the most efficient way of producing these images for analysis. This is generally the preferred method because:

• It reduces the amount of data being generated or stored in the first place, especially if we don't intend to treat the images as a 3D stack afterwards.
• Generating a MIPs in arivis is not automated, meaning that we have to actively convert each stack into their respective MIPs. This can be especially time consuming for large datasets that contain multiple fields of view.
• The process of generating a MIP in arivis creates a new file or image set within the existing document, leading to some redundancy in storage or the potential need to do a lot of manual tidying up to remove the uncompressed stacks.
• When dealing with large datasets with multiple image sets, if we save the MIPs as new documents it can lead to a large number of documents to be processed, and if we save the MIPs as new image sets it leads to large files with a large number of sets that will need to be actively selected or removed from the selection for batch processing.

Having said all this, arivis Pro can produce Maximum Intensity Projections from the Projection Viewer.