Cellpose is a powerful segmentation tool for bioimage analysis, and it is free to use and does not require commercial software like Vision4D. However, there are advantages to using cellpose within Vision4D pipelines.

The first main advantage of using cellpose in Vision4D was alluded to above. This implementation allows users to use the method with images of virtually any size on virtually any computer that runs MS Windows. It can therefore be used to segment very large 2D and 3D datasets like slide scans and Light-Sheet scans.

The second advantage of using cellpose in Vision4D is the ability to use it in conjunction with other pipeline operations to refine the results, extract additional information, and enable easy-to-use visualization tools to both review and present the results of analyses.

Building complex pipelines that use cellpose, users can:

• Use pre-segmentation enhancements to create more easily segmented images
• Refine the results of the segmentation to remove segmentation artifacts like small/large objects that shouldn't be segmented, 
• Use cellpose segmentation results together with traditional segmentation tools to identify inter-object relationships like finding children objects inside cells or distances to neighbors

Many of these possibilities are covered in the User Guide that users can access from the help menu, and in other articles on this website. Please use the search tool to find out more about compartments analysis, object coloring options, movie making, etc.

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