Troubleshooting Dense Cloud Issues in Metashape: Holes, Noise & Misalignment Fixes

The dense cloud is a critical step in Agisoft Metashape’s photogrammetry pipeline. But when things go wrong—such as holes, noise, or poor alignment—the quality of your final 3D model or orthomosaic suffers. In this guide, we’ll walk through common dense cloud issues in Metashape and show you how to troubleshoot and fix them for better results.

1. What Is the Dense Cloud in Metashape?

The dense cloud is a collection of 3D points generated from multiple overlapping photos using depth maps. It is used to create textured meshes, digital elevation models (DEM), and orthomosaics. Errors in this step can cascade into later stages.

2. Common Problems in Dense Cloud Generation

• Holes: Missing points in certain areas
• Noise: Floating or scattered points not part of the actual geometry
• Misalignment: Offset point clouds or tilted objects
• Blurry geometry: Soft or distorted shapes

3. Causes and Fixes: Holes in Dense Cloud

Cause: Insufficient image coverage, lack of tie points, or strong shadows.

• Capture more photos with better overlap (ideally 80% front and 70% side).
• Use multi-angle shots to cover underhangs or vertical surfaces.
• Ensure well-lit environments and avoid reflective or transparent surfaces.
• Try increasing the Quality setting in “Build Dense Cloud” to High.
• Manually mask problematic areas in photos before processing.

4. Causes and Fixes: Noise and Floating Points

Cause: Poor photo texture, moving objects, or aggressive depth filtering settings.

• In Build Dense Cloud, set Depth Filtering to Moderate or Aggressive.
• Use Gradual Selection → Reconstruction Uncertainty or Projection Accuracy to clean sparse cloud before dense generation.
• Mask or remove images with motion blur, overexposure, or low contrast.
• After dense cloud generation, use Tools → Dense Cloud → Select Points by Color/Region to delete noise manually.

5. Causes and Fixes: Misalignment and Tilt

Cause: Poor alignment of photos, GPS drift, or lack of ground control.

• Re-align photos with higher key point limit (e.g. 40,000) and correct accuracy (Medium/High).
• Use Reference tab to manually adjust camera locations if GPS is inconsistent.
• Add Ground Control Points (GCPs) for proper scaling and orientation (Pro version).
• Use Optimize Cameras after alignment and before building dense cloud.

6. Tips for Cleaner Dense Clouds

• Use high-resolution, sharp, and well-lit images.
• Lock camera settings (exposure, focus) to avoid variation.
• Disable auto-exposure and auto-white balance on drones and DSLRs.
• Fly at lower altitudes for increased image detail (within legal limits).
• Avoid images with motion blur or objects like trees blowing in the wind.

7. Tools to Clean Dense Cloud in Metashape

• Gradual Selection: Ideal for removing outliers in sparse cloud before dense generation.
• Manual Selection: Use rectangle or lasso to delete noise post-processing.
• Classify Ground Points: Helps separate terrain from structures.
• Duplicate Chunk: Before editing, duplicate the chunk so you can revert if needed.

8. When to Regenerate the Dense Cloud

If you’ve improved the photo alignment, added masks, or corrected the sparse point cloud, it’s best to re-run the dense cloud step. Delete the existing cloud and rebuild it using optimized settings.

Conclusion

Dense cloud issues in Metashape are common but fixable. Whether you’re dealing with holes, noise, or misalignment, most problems can be solved with better image input, proper settings, and some manual cleanup. Mastering this step is essential for producing accurate 3D models, DEMs, and orthomosaics in professional workflows.