Maximum Intensity Projection (MIP) renders your dataset directly in the 3D viewport. It is similar to meshes, giving you a spatial view of your data, but it applies to any image layer rather than only segmentations, and it needs no precomputation. Technically, MIP looks through the volume and keeps the brightest value along each line of sight, so fluorescent labels and other bright structures stand out in three dimensions.
MIP is part of our ongoing work to improve WEBKNOSSOS for light microscopy datasets, and it is available now.
Confocal microscopy dataset rendered with MIP in WEBKNOSSOS. Data by Blin et al., PLOS Biology 2019
To turn it on, open the bounding box menu and pick the layers you want to render as a maximum intensity projection.
Opening the bounding box menu and selecting layers to render as MIP
In the MIP settings, adjust the ray marching steps to control how finely WEBKNOSSOS samples through the volume: more steps for a smoother, more detailed rendering, fewer for faster interaction.
Adjusting the ray marching steps slider in the MIP settings
If you're working with meshes, enable depth-correct rendering so that meshes and the projected volume respect each other in space — a mesh behind a bright structure stays correctly hidden instead of floating on top.
Depth-correct rendering with meshes
Whether you're exploring a new dataset, checking your labels, or putting together a figure, MIP gives you a fast, intuitive way to see your data in three dimensions.
Watch the full walkthrough on YouTube , and try it out at webknossos.org.
. . .
This feature was developed with support from St. Jude Children's Research Hospital.