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Exercise 3: The Basics of CloudCompare

(Allow at least 1 hour for Exercise 3)

A step-by-step video guide to Exercise 3 can be found here.

Meshlab allowed us to quickly visualise the datasets and take simple measurements from the 3D models to familiarise ourselves with the dataset. To take our analysis to the next step, we will use a different software tool which is more intuitive and has better functionality for isolating individual features, CloudCompare. In this exercise you will learn to:

Using Cloud Compare

CloudCompare is another free software package that is useful in working with and analysing 3D datasets. Only a few basic functions will be discussed here, but CloudCompare's User’s Manual is virtually comprehensive in describing its many uses. In some ways, it is more intuitive than MeshLab, although creating a visualisation as informative as the ‘Radiance Scaling’ shader from MeshLab in CloudCompare requires more work.

One big difference between CloudCompare and MeshLab is that, while you can work with 3D meshes in CloudCompare, the software was initially designed to work with point clouds, as the name ‘CloudCompare’ suggests. As described above in the introduction of this document, the point cloud is the cluster of individual points that are recorded by a 3D recording technique, whether this was by photogrammetry, structured light scanning, or laser scanning. Some of CloudCompare’s functions will use the vertices of the mesh as ‘point clouds’. This will be particularly important in Exercises 4 and 5.

What is a ‘morphometric parameter’? What do they tell us?

Morphometric parameters are quantitative measurements that can be used to describe an object’s form. This includes measurements you will already be familiar with (length, width, volume), but can also include parameters like ‘Roughness’ or ‘Curvature’. By incorporating these parameters, features that would otherwise be difficult to see on the physical object become much more obvious when applied to the 3D model. In Exercise 3, we will begin with using the Z coordinates, which represent the relative height of the mesh surface.

Shaders vs Morphometrics While they can both be used to visualise data, Shaders function differently from Morphometric Parameters. As noted above in Exercise 1, Shaders take multiple factors into their calculation, including: lighting position and transparency, view position, material properties, and the shape of the 3D surface. Morphometrics are simpler in that they only take into account the shape of the 3D surface; however, there are a wide variety of morphometric parameters that can be used in morphometrics (height, length, width, roughness, curvature) and can be used in quantitative applications, which will be explored more fully in Exercises 4 and 5.

Roughness and Curvature ‘Roughness’ and ‘Curvature’ are calculated using statistics. As defined by CloudCompare…

Both of these calculations rely on a ‘nearest neighbours’ approach. While this concept can be applied differently in different fields, essentially the software determines whether a point is ‘different’ by looking at its neighbours within a given radius defined by the user. If a point’s elevation is quite similar compared to the plane formed by its neighbouring points, it will not be attributed to a high ‘roughness’ value.

Getting Started

  1. To start, ‘Open’ both of the .stl files from PH 13 (you can also use Ctrl+O). Your screen should look something like the image below.

A screenshot of the CloudCompare interface with both scans of PH 13

  1. In the top left section of the workspace, you can see a window that says ‘DB Tree’ at the top (which is short for ‘DataBase Tree’). This is where you can see the files you have added to the project. Currently, the two .stl files we have imported are two separate entities. To merge the two files into one 3D entity, Ctrl+Click both of the ‘Mesh’ layers from each of the files so that these are both highlighted. Then, find and click the ‘Merge multiple clouds’ icon on the toolbar (highlighted with a red box below). Then, uncheck the boxes to the left of the original files so that only the new ‘Merged Mesh’ is visible.

This image shows the CloudCompare interface and shows how to merge two
meshes into a single mesh using the 'Merge Multiple Clouds' icon. This
icon is highlighted with a red box in the

  1. Rotating the mesh is slightly different in CloudCompare, as the trackball is not constantly visible. Click and hold the mesh – the trackball will appear. Try moving your mouse to rotate the mesh. As you are moving the mesh, take note of the appearance of the fingerprint(s?). Let’s try isolating the fingerprints using the ‘Segment’ tool in CloudCompare.

Try it yourself!

Segmenting in CloudCompare

  1. To do anything to alter the mesh, the ‘Merged Mesh’ will need to be highlighted in the DB Tree. The ‘Segment’ tool appears as a pair of scissors in the toolbar above the viewing window. Once you have selected the ‘Segment tool’, your screen should look something like that pictured below. As it says above the 3D model, left click around the fingerprints to add points to the polygon, and right click when you are happy with the shape you have created. Then, click the ‘Segment in’ to delete everything around the area you have selected.

This image shows the CloudCompare interface with the merged mesh of PH
13 visible. The segment tool (highlighted with a red box and label on
the toolbar) has been selected, so a new toolbar has appeared in the top
right corner of the screen. After selecting the region of the
fingerprint, the 'segment in' option can be selected (again,
highlighted in a red box and

  1. Once you have selected ‘Segment In’, the Segmentation function will pause. You can now rotate the area you have selected to ensure you are happy with the results. If the area needs further editing, unpause the tool to continue segmenting. If you are satisfied with the results, click the checkmark in the Segment Toolbar to ‘Confirm Segmentation’.

  2. After confirming the segmentation, notice that the ‘Merged Mesh’ in the DB Tree has divided into two meshes: ‘Merged Mesh.remaining’ and ‘Merged Mesh.part’. Toggle each of these by clicking in the checkbox for each. You will see that your selected area has now been segmented from the rest of the 3D data. Turn off the ‘Merged Mesh.remaining’ layer to continue working with your fingerprint data.

Note: For better visualisation results, ensure that you have segmented each of the prints from each other so that you are only working with one print at a time. To rename the meshes in the DB Tree, double left click on the object name you wish to change (highlighted in red below).

In Cloud Compare, a single fingerprint from PH 13 has been segmented
from the rest of the mesh. In the Database Tree, a red rectangle
highlights that users should double click on the file name to rename the

Visualising 3D models in CloudCompare

Before making substantial edits, it is always a good idea to duplicate/clone the dataset you will be working with so that, if something goes wrong, you will not have to repeat the above steps each time. Highlight the Merged mesh.part and click the ‘Clone’ button (the icon shows two sheep, outlined in a red box below). If you want to save the work you have done in CloudCompare, you need to be sure that [all components] you want to save are highlighted in the DB Tree before you select ‘Save’ (you select multiple files/folders by holding down the ‘Ctrl’ button and clicking on the files you wish to save in the DB Tree).

An image of part of the CloudCompare toolbar. The 'Clone' icon is
highlighted with a red

  1. First, it is important that the fingerprint is as ‘flat’ as it can be in the 3D space, so that the software can recognise the high points and low points of the ridges (aligning the height of the ridges to represent the Z coordinates). From the toolbar on the left side of the screen, select the icon that looks like a black triangle and an arrow. The software will then prompt you to select three points on the 3D mesh. Ensure that these points are as far apart as possible on the mesh, along the edge, as this will determine how flat the print is.

A part of another toolbar is presented here with a red rectangle
highlighting the icon that would allow users to pick three points on the
mesh to level the mesh. A snapshot of the 'pick three points'
levelling option in

  1. An automated option for levelling the mesh is provided under ‘Tools’, called ‘Fit’ to plane. This produces a transformation matrix in the ‘Console’ area of the screen (usually at the bottom of the window) that will align your mesh to the plane it has calculated. A matrix is an array that, in this case, dictates how the mesh needs to be mathematically rotated and translated to align with the plane. The first three columns correspond to how the points should rotate in three dimensions, while the fourth column corresponds to how much and in what direction the mesh needs to slide, or translate.

  2. To apply this alignment, click on the matrix entry so that it is highlighted and use Ctrl+C to copy the matrix. Ensure that the mesh is highlighted in the DB tree. Navigate to the ‘Edit’ dropdown menu to find the ‘Apply Transformation’ function, delete the matrix provided and paste your new matrix in using Ctrl+V. Click ‘OK’ and the transformation will be complete. Uncheck the tick box next to the ‘Plane’ that was generated to remove it from view.

This image shows how to apply the transformation if using the 'Fit to
plane' levelling option. It shows where to find the transformation
matrix in the console portion of the CloudCompare

A screenshot showing where to paste the transformation

After the transformation has been applied, check the box next to the
plane to remove it from

  1. Once the 3D model is aligned, navigate to ‘Scalar Fields’ from the ‘Edit’ dropdown menu and select ‘Export coordinate(s) to SF(s)’. Ensure that the checkbox next to ‘Z’ is selected before you hit ‘Ok’. A Scalar Field, as defined in the CloudCompare manual, is ‘a set of values (one value per point)’; CloudCompare allows a value associated with a point/vertex to be displayed as colours or have filters or basic math operations applied to them. In this case, we are assigning the Z-values of the mesh as a scalar field – the relative height of the mesh above the level plane we created in the previous step(s). This will allow us to assign different colours to points with different heights. This is only one of many values that could be assigned to a Scalar Field; virtually any property that can be used to describe the shape of the surface can appear in the scalar field, including other morphometric parameters that will be introduced in Exercises 4 and 5.

A screenshot showing the interface to export the Z coordinates of the
3D model to the Scalar

  1. If you highlight the 3D model and navigate to the ‘Properties’ window (often automatically pinned below the DB Tree window), you will find that under ‘CC Object’ you can now change the ‘Colors’ from ‘None’ to ‘Scalar field’. Scrolling through the properties, under ‘Color Scale’, you will be able to change the appearance of the 3D model from a dropdown menu.

A screenshot of the Properties window to show how to set the Scalar
field as the color of the 3D

A screenshot of the fingerprint mesh with its color set to Scalar
field and a Viridis color scale

  1. From the SF display params, using the Viridis setting (above), you can see that the highest values are yellow, while the lowest values are purple. This does not quite show the fingerprint at its best, though it clearly shows the ridge of raised clay in the centre of the print. To edit the colour scale, navigate to the icon for the ‘Color Scale Editor’ in the toolbar across the top of the screen. To edit any of the scales, you will first need to make a copy of the base color scale you start with. Choose to make a copy of the ‘Grey’ preset colours, rename the scale, and save it. Now set your new scale as the current color scale.

A close up of the CloudCompare toolbar with the Color Scale
Editor/Manager icon highlighted with a red

A screenshot showing the Color Scale Editor prior to copying the Grey
color scale.

A screenshot of the mesh with a grey color scale applied.


  1. Now go back and edit your edited scalar field. On the color bar, you will see two small boxes at either end of the bar. Click on the black box on the left – you will see that the fields below this, in an area labelled ‘Selected Slider’, are now no longer greyed out. Change the colour of this end of the slider by clicking the box next to ‘Color’. For now, change this to white.

A screenshot of edits being made to the copied color

  1. Now change the slider on the right side of the bar to black. Click apply and save the modifications.

  2. Your screen should look something like the image below, with the black and white gradient inverted from its previous state. In the properties of the mesh, in the SF display params, experiment with sliding the triangles along the histogram to see how this affects the coloration of the 3D model.

A screenshot of the fingerprint where the grey color scale has been
inverted. Now the raised ridge of clay is black, while the lower parts
of the mesh are white.

  1. While the above image appears more similar to how we might visualise a fingerprint, the raised ridge of clay along the centre is clearly affecting how this is being visualised. If one were to compare this against some of the options in Meshlab’s Radiance Scaling (see below; the red areas highlight the raised ridges of the fingerprint), it is clear that the added topography from the ridge and the curvature of the ceramic vessel itself is diminishing the impact of the relative difference in height (the Z coordinates of the 3D model) between the fingerprint ridges and the dips between them.

A screenshot of the same fingerprint mesh imported into Meshlab.
Radiance Scaling has been applied, but the display mode has been changed
to Colored Descriptor. This brings out the ridges of the fingerprint
despite the raised ridge of clay disrupting the centre of the

Reflect and Write

Try it yourself!

A screenshot of one of the fingerprint meshes run through the Fingerprint Minutiae Viewer software. Features potentially key to fingerprint identification have been highlighted with green rectangles.

A step-by-step video guide to Exercise 3 can be found here.

Back to Exercise 2 To Exercise 4: Quantitative Approaches to Interpretation