Watch: 3D profilometry of a SawBone tibial plateauMapping and analysis · 0:24
3D profilometry of a SawBone tibial plateau
A demonstration of 3D profilometry on a SawBone tibial plateau using the Mach-1.
Test configurations
Profilometry (3D)
Historically, profilometry was acknowledged as a graph of the surface height as the surface is moved relative to the contact profilometer's stylus (skating on the surface). This notion is changing with the emergence of numerous non-contact (optical) profilometry techniques, where surface height is mapped on a XY grid (e.g. through laser beam triangulation). Using a multiaxial mechanical tester, a similar non-destructive characterization can be performed by scanning the surface with series of very light contacts with the surface. At each location, a small spherical indenter is lowered against the surface until a predefined load is detected by the load cell (as low as few uN). The vertical position of the indenter at the first contact detection is the local height of the surface. Depending of the tester specifications, a submicron resolution can be achieved on samples with a wide range of stiffness (few kPa to hundreds of GPa). This technique is not influenced by optical artifacts and can be performed with the sample bathing in a solution.
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FAQ
How is a surface positioning template created?
In order to facilitate eventual comparison between samples with similar surface, it is recommended to use a boundaries (surface positioning) template to standardize their positioning in the picture frame. This surface positioning template is a “.map” file containing a list of positions outlining the sub-surface’s boundaries and a reference image of the surface of interest.
The reference image should be considered as a representative (average) image of the different samples with a similar surface that will be used for the display of average mapping results taken from multiple comparable surfaces. In order to be representative (average) of all sample surface boundaries within the group of interest, template must be created using enough independent sample surface images. Of course, the number of independent images required will be a function of the extent of boundary variation within the group. Image processing software shall be used to create the representative (average) image.
The boundaries (surface positioning) template can be modified from time to time, in particular when data collection indicates that it is not representative of the population. For this reason, a version number is added to the template which is named using the following convention: “Template-X_SurfaceDescription_vV.map”, where X is the left (L) or right (R) side and V is the version number.
The following is the list of the left and right surface positioning templates currently available:
• Human: Distal Femur, Femoral Condyles, Tibial Plateau, Patella
• Sheep: Femoral Condyles, Tibial Plateau
• Rabbit: Femoral Condyles, Tibial Plateau
• Rat: Femoral Condyles, Tibial Plateau
• Mouse: Femoral Condyles, Tibial Plateau
NOTE. If the sample presents closed sub-surfaces (for example an entire tibial plateau with the medial and lateral plateaus), it is important to describe each of these regions of interest (sub-surfaces) in order to interpolate the mapping within the delimited boundaries.
1. Position the sample in the camera feed or place the camera towards a screen in order to visualize a representative (single or average) image of the sample in the camera feed. Ideally, sample’s surface should be at the center and occupies the maximum space in the image frame while remaining completely visible and allowing some clearance for eventual refraction compensation, if applicable.
2. Create the boundary of the sample surface in the camera feed. Note that it is important to edit/select a sub-surface in the Sub-SurfaceID field before adding a boundary in order to assign the boundary to a sub-surface.
2.1 Choose “Boundary” in “View” of the menu bar to see boundaries in the camera feed.
2.2 Edit the Sub-Surface ID field as defined in the associated protocol.
2.3 Choose “Add Boundary” in “Edit” of the menu bar and click in the camera feed to define the boundary along the sample sub-surface and a closed contour will be created.
2.4 If necessary, choose “Delete Boundary” in “Edit” of the menu bar and click in the camera feed at a boundary point along the sample sub-surface and the closed contour will be reshaped consequently.
2.5 Repeat steps 2.2 to 2.4 for each sub-surface of the sample.
3. Create a blank .map file and name it using the following convention: “Template-X_SurfaceDescription_vV.map”, where X is the left (L) or right (R) side and V is the version number.
The reference image should be considered as a representative (average) image of the different samples with a similar surface that will be used for the display of average mapping results taken from multiple comparable surfaces. In order to be representative (average) of all sample surface boundaries within the group of interest, template must be created using enough independent sample surface images. Of course, the number of independent images required will be a function of the extent of boundary variation within the group. Image processing software shall be used to create the representative (average) image.
The boundaries (surface positioning) template can be modified from time to time, in particular when data collection indicates that it is not representative of the population. For this reason, a version number is added to the template which is named using the following convention: “Template-X_SurfaceDescription_vV.map”, where X is the left (L) or right (R) side and V is the version number.
The following is the list of the left and right surface positioning templates currently available:
• Human: Distal Femur, Femoral Condyles, Tibial Plateau, Patella
• Sheep: Femoral Condyles, Tibial Plateau
• Rabbit: Femoral Condyles, Tibial Plateau
• Rat: Femoral Condyles, Tibial Plateau
• Mouse: Femoral Condyles, Tibial Plateau
NOTE. If the sample presents closed sub-surfaces (for example an entire tibial plateau with the medial and lateral plateaus), it is important to describe each of these regions of interest (sub-surfaces) in order to interpolate the mapping within the delimited boundaries.
1. Position the sample in the camera feed or place the camera towards a screen in order to visualize a representative (single or average) image of the sample in the camera feed. Ideally, sample’s surface should be at the center and occupies the maximum space in the image frame while remaining completely visible and allowing some clearance for eventual refraction compensation, if applicable.
2. Create the boundary of the sample surface in the camera feed. Note that it is important to edit/select a sub-surface in the Sub-SurfaceID field before adding a boundary in order to assign the boundary to a sub-surface.
2.1 Choose “Boundary” in “View” of the menu bar to see boundaries in the camera feed.
2.2 Edit the Sub-Surface ID field as defined in the associated protocol.
2.3 Choose “Add Boundary” in “Edit” of the menu bar and click in the camera feed to define the boundary along the sample sub-surface and a closed contour will be created.
2.4 If necessary, choose “Delete Boundary” in “Edit” of the menu bar and click in the camera feed at a boundary point along the sample sub-surface and the closed contour will be reshaped consequently.
2.5 Repeat steps 2.2 to 2.4 for each sub-surface of the sample.
3. Create a blank .map file and name it using the following convention: “Template-X_SurfaceDescription_vV.map”, where X is the left (L) or right (R) side and V is the version number.
How can I dimension the top view image of my sample to perform a mapping?
In order to dimension the sample and calibrate its image, two reference marks need to be created on the sample surface as far as possible from each other (ideally not over regions of interest). Marks should be made at approximately the same surface height (ideally at the average horizontal mapping plane, the focal plane of the camera), since it is the top-view image of the sample that is calibrated.
NOTE. Different specified methods can be used to create those reference marks, but they should be made as small as possible (while being clearly visible on the sample and eventually on its image) and should remain mechanically stable and visible after immersion in saline solution (if applicable) and sample manipulation. For example, adding a small drop of India ink over a needle puncture of the cartilage layer at the boundary of the articular surface have proven to lead to good results. It might also be possible to use two distant, clear and unambiguous sample landmarks as reference marks.
1. If already created, open the blank “Filename.map” file to be converted into metric coordinates. Note that the corresponding image “Filename.jpg” should present two visible reference marks. If not already created and if the sample is still in the camera feed, add two reference indicators on the two visible reference marks.
1.1. Choose “Reference 1 (red)” in “Edit” of the menu bar and click in the camera feed at the first reference mark.
1.2. Choose “Reference 2 (blue)” in “Edit” of the menu bar and click in the camera feed at the second reference mark.
2. Set the metric values of the reference marks.
2.1. Choose “Calibration” in “Edit” of the menu bar.
2.2. Report the X and Y metric coordinates of the reference 1 and reference 2 in the “Calibration” pop-up window according to a specific method, currently available is the “Mach-1” method.
“Mach-1” method: This method allows converting the pixels coordinates of the positions into metric coordinates that will be used for a mechanically-controlled surface mapping with the 2 horizontal stages of a multi-axial Mach-1 mechanical tester. The coordinate system used in this method corresponds to the Mach-1 horizontal stages where it is preferable to set X and Y origin at the first reference mark. With the sample/testing chamber mounted onto the Mach-1, move the stages in such a way that the center of the Mach-1’s indenter (its vertical axis) is positioned just over the first reference mark (red indicator), set the position of the X and Y stage to zero position. Repeat the same procedure for the second reference mark (blue indicator), report the X and Y stage position in the “Calibration” pop-up window. Note that since it is possible to increase the effective scanning area (limited by the stages) of the Mach-1 by manually rotating/repositioning the sample or sample/chamber assembly, a configuration index “i” is added to this characterization (by default i=1). Note that it is recommended to keep this configuration index (i) in all Mach-1 raw data generated under configuration (i).
3. Create a “Filename-Dimensioning.map” file, where “Filename” can be defined in an associated protocol.
3.1. Verify that reference 1 and reference 2 indicators are displayed in the camera feed and that their metric coordinates (according to the chosen method) has been reported in the “Calibration” pop-up window.
3.2. Choose “Create .map” in “File” of the menu bar and all positions, boundaries and references displayed in the camera feed will be saved in the .map file and a snapshot image “.jpg” of the camera feed will be saved in the same folder. Also, two characterizations “ScanX(mm)” and “ScanY(mm)” containing the metric coordinates of the two reference marks and those of each position of the grid will be saved.
1. If already created, open the blank “Filename.map” file to be converted into metric coordinates. Note that the corresponding image “Filename.jpg” should present two visible reference marks. If not already created and if the sample is still in the camera feed, add two reference indicators on the two visible reference marks.
1.1. Choose “Reference 1 (red)” in “Edit” of the menu bar and click in the camera feed at the first reference mark.
1.2. Choose “Reference 2 (blue)” in “Edit” of the menu bar and click in the camera feed at the second reference mark.
2. Set the metric values of the reference marks.
2.1. Choose “Calibration” in “Edit” of the menu bar.
2.2. Report the X and Y metric coordinates of the reference 1 and reference 2 in the “Calibration” pop-up window according to a specific method, currently available is the “Mach-1” method.
“Mach-1” method: This method allows converting the pixels coordinates of the positions into metric coordinates that will be used for a mechanically-controlled surface mapping with the 2 horizontal stages of a multi-axial Mach-1 mechanical tester. The coordinate system used in this method corresponds to the Mach-1 horizontal stages where it is preferable to set X and Y origin at the first reference mark. With the sample/testing chamber mounted onto the Mach-1, move the stages in such a way that the center of the Mach-1’s indenter (its vertical axis) is positioned just over the first reference mark (red indicator), set the position of the X and Y stage to zero position. Repeat the same procedure for the second reference mark (blue indicator), report the X and Y stage position in the “Calibration” pop-up window. Note that since it is possible to increase the effective scanning area (limited by the stages) of the Mach-1 by manually rotating/repositioning the sample or sample/chamber assembly, a configuration index “i” is added to this characterization (by default i=1). Note that it is recommended to keep this configuration index (i) in all Mach-1 raw data generated under configuration (i).
3. Create a “Filename-Dimensioning.map” file, where “Filename” can be defined in an associated protocol.
3.1. Verify that reference 1 and reference 2 indicators are displayed in the camera feed and that their metric coordinates (according to the chosen method) has been reported in the “Calibration” pop-up window.
3.2. Choose “Create .map” in “File” of the menu bar and all positions, boundaries and references displayed in the camera feed will be saved in the .map file and a snapshot image “.jpg” of the camera feed will be saved in the same folder. Also, two characterizations “ScanX(mm)” and “ScanY(mm)” containing the metric coordinates of the two reference marks and those of each position of the grid will be saved.
What is the procedure to create a blank “.map” file?
NOTE. If no testing chamber is used proceed to step 5.
1. Completely screw the sample holder into the testing chamber and place the sample over it. If applicable, center the sample relative to the holder and rotate it in such a way that its orientation will approximately correspond to that of the corresponding surface positioning template image when seen by the technician in front of the testing chamber. Using a black marker, draw a mark on the top of the sample holder that will be used for the repositioning of the sample over the holder.
2. Remove the sample and unscrew the sample holder.
3. Depending on the sample type, a sample has to be attached to the sample holder following an appropriate method, either with screws and/or cyanoacrylate glue (recommended: Loctite 4013).
“Screws” method: In the case of sample holder (a – see Figure 1a), place the flat sample side in firm contact with the sample holder. Secure it with at least 2 screws from the bottom side. Make sure that the screws remain at least 1 cm away from the surface. In the case of sample holder (b – see Figure 1b), place the flat sample side in firm contact with the sample holder. Secure it from the periphery using its 6cone-ended screws. In the case of sample holder (c – see Figure 1c), place the sample in the middle. Secure it with its 2 screws.
“Glue” method: In the case of any sample holder with a flat portion (see Figure 1), make sure that the bottom surface of the sample and the flat portion of the sample holder are dry to ensure a good adherence. In the case of articular surfaces, apply the glue on the sample bottom (the bony part) and be careful not to touch the cartilage surface. If by mistake the glue touches the sample, try to clean the surface by using a flux of PBS, and report approximately the touched area in the laboratory book. The glued sample should be maintained for at least 1 minute to ensure a good adherence.
4. Screw the assembly into the testing chamber.
5. If required, create two reference points on the surface as per the “Calibration of the sample” section. If required, measure the horizontal distance between the references with a calibrated caliper and report the value (ideally, at a location specified in an associated protocol).
6. Adjust the position of the camera and its focus in such a way that the sample’s surface occupies the maximum space in the live camera feed while remaining completely visible by keeping a margin of about 5% at the 4 sides (right, left, up and down) to accommodate an eventual water refraction compensation, if applicable. It is recommended to use an appropriate surface positioning template to facilitate eventual mapping comparison between samples.
6.1. Choose “Import .map” in “File” of the menu bar.
6.2. Select the corresponding surface positioning template (*.map) and boundaries will be displayed by a closed contour (solid line) in the camera feed.
6.3. Adjust the position of the camera and its focus in such a way that the sample’s surface boundaries fit those of the surface positioning template.
7. Superimpose a position grid to the sample image. Positions could be added one by one according to a snapping grid (aligned) or anywhere on the sample. Also, positions could be imported through a previously created .map file. Note that it is important to edit/select a sub-surface in the Sub-SurfaceID field before adding a position in order to assign the position to a sub-surface.
7.1 If applicable, choose “Import .map” in “File” of the menu bar and select the corresponding position grid and the positions will be displayed by a circled marker in the camera feed.
7.2 If applicable, choose “Grid” in “View” of the menu bar to display a grid of snapping dots in the camera feed.
7.3 Edit the Sub-Surface ID field as defined in the associated protocol.
7.4 Choose “Add Positions” in “Edit” of the menu bar and click in the camera feed to add positions at each location of interest on the sample sub-surface.
7.5 If necessary, choose “Delete Positions” in “Edit” of the menu bar and click in the camera feed at each position that is not overlaid on a location of interest on the sample sub-surface and the position will be deleted from the camera feed.
7.6 Repeat steps 7.3 to 7.5 for each sub-surface of the sample.
8. If required, create the specific boundary of the sample sub-surfaces in order to refine the outline of the mapping surface for this specific sample (using at least 30 boundary points). If needed, surface boundary layer from the positioning template can be deleted first. Note that this step is important for the interpolation of characterization values to the boundary to obtain a complete mapping of the sample surface. Note that it is important to edit/select a sub-surface in the Sub-SurfaceID field before adding a boundary in order to assign the boundary to a sub-surface.
8.1. Choose “Boundary” in “View” of the menu bar to see boundaries in the camera feed.
8.2. Edit the Sub-Surface ID field as defined in the associated protocol.
8.3. Choose “Add Boundary” in “Edit” of the menu bar and click in the camera feed to define the boundary along the sample sub-surface and a closed contour will be created.
8.4. If necessary, choose “Delete Boundary” in “Edit” of the menu bar and click in the camera feed at a boundary point along the sample sub-surface and the closed contour will be reshaped consequently.
8.5. Repeat steps 8.2 to 8.4 for each sub-surface of the sample.
9. If required, add reference indicators on the two reference marks previously created at step 5.
9.1. Choose “Reference 1 (red)” in “Edit” of the menu bar and click in the camera feed at the first reference mark.
9.2. Choose “Reference 2 (blue) in “Edit” of the menu bar and click in the camera feed at the second reference mark.
10. Create this blank “Filename.map” file, where “Filename” is standardized filename format that it is recommended to define in an associated protocol (refer to Appendix I for a recommended file naming convention). When filename standardization is not necessary, any name can be used as “Filename”. Choose “Create .map” in “File” of the menu bar and all positions, boundaries and references displayed in the camera feed will be saved in the .map file and a snapshot image “.jpg” of the camera feed will be saved in the same folder.
1. Completely screw the sample holder into the testing chamber and place the sample over it. If applicable, center the sample relative to the holder and rotate it in such a way that its orientation will approximately correspond to that of the corresponding surface positioning template image when seen by the technician in front of the testing chamber. Using a black marker, draw a mark on the top of the sample holder that will be used for the repositioning of the sample over the holder.
2. Remove the sample and unscrew the sample holder.
3. Depending on the sample type, a sample has to be attached to the sample holder following an appropriate method, either with screws and/or cyanoacrylate glue (recommended: Loctite 4013).
“Screws” method: In the case of sample holder (a – see Figure 1a), place the flat sample side in firm contact with the sample holder. Secure it with at least 2 screws from the bottom side. Make sure that the screws remain at least 1 cm away from the surface. In the case of sample holder (b – see Figure 1b), place the flat sample side in firm contact with the sample holder. Secure it from the periphery using its 6cone-ended screws. In the case of sample holder (c – see Figure 1c), place the sample in the middle. Secure it with its 2 screws.
“Glue” method: In the case of any sample holder with a flat portion (see Figure 1), make sure that the bottom surface of the sample and the flat portion of the sample holder are dry to ensure a good adherence. In the case of articular surfaces, apply the glue on the sample bottom (the bony part) and be careful not to touch the cartilage surface. If by mistake the glue touches the sample, try to clean the surface by using a flux of PBS, and report approximately the touched area in the laboratory book. The glued sample should be maintained for at least 1 minute to ensure a good adherence.
4. Screw the assembly into the testing chamber.
5. If required, create two reference points on the surface as per the “Calibration of the sample” section. If required, measure the horizontal distance between the references with a calibrated caliper and report the value (ideally, at a location specified in an associated protocol).
6. Adjust the position of the camera and its focus in such a way that the sample’s surface occupies the maximum space in the live camera feed while remaining completely visible by keeping a margin of about 5% at the 4 sides (right, left, up and down) to accommodate an eventual water refraction compensation, if applicable. It is recommended to use an appropriate surface positioning template to facilitate eventual mapping comparison between samples.
6.1. Choose “Import .map” in “File” of the menu bar.
6.2. Select the corresponding surface positioning template (*.map) and boundaries will be displayed by a closed contour (solid line) in the camera feed.
6.3. Adjust the position of the camera and its focus in such a way that the sample’s surface boundaries fit those of the surface positioning template.
7. Superimpose a position grid to the sample image. Positions could be added one by one according to a snapping grid (aligned) or anywhere on the sample. Also, positions could be imported through a previously created .map file. Note that it is important to edit/select a sub-surface in the Sub-SurfaceID field before adding a position in order to assign the position to a sub-surface.
7.1 If applicable, choose “Import .map” in “File” of the menu bar and select the corresponding position grid and the positions will be displayed by a circled marker in the camera feed.
7.2 If applicable, choose “Grid” in “View” of the menu bar to display a grid of snapping dots in the camera feed.
7.3 Edit the Sub-Surface ID field as defined in the associated protocol.
7.4 Choose “Add Positions” in “Edit” of the menu bar and click in the camera feed to add positions at each location of interest on the sample sub-surface.
7.5 If necessary, choose “Delete Positions” in “Edit” of the menu bar and click in the camera feed at each position that is not overlaid on a location of interest on the sample sub-surface and the position will be deleted from the camera feed.
7.6 Repeat steps 7.3 to 7.5 for each sub-surface of the sample.
8. If required, create the specific boundary of the sample sub-surfaces in order to refine the outline of the mapping surface for this specific sample (using at least 30 boundary points). If needed, surface boundary layer from the positioning template can be deleted first. Note that this step is important for the interpolation of characterization values to the boundary to obtain a complete mapping of the sample surface. Note that it is important to edit/select a sub-surface in the Sub-SurfaceID field before adding a boundary in order to assign the boundary to a sub-surface.
8.1. Choose “Boundary” in “View” of the menu bar to see boundaries in the camera feed.
8.2. Edit the Sub-Surface ID field as defined in the associated protocol.
8.3. Choose “Add Boundary” in “Edit” of the menu bar and click in the camera feed to define the boundary along the sample sub-surface and a closed contour will be created.
8.4. If necessary, choose “Delete Boundary” in “Edit” of the menu bar and click in the camera feed at a boundary point along the sample sub-surface and the closed contour will be reshaped consequently.
8.5. Repeat steps 8.2 to 8.4 for each sub-surface of the sample.
9. If required, add reference indicators on the two reference marks previously created at step 5.
9.1. Choose “Reference 1 (red)” in “Edit” of the menu bar and click in the camera feed at the first reference mark.
9.2. Choose “Reference 2 (blue) in “Edit” of the menu bar and click in the camera feed at the second reference mark.
10. Create this blank “Filename.map” file, where “Filename” is standardized filename format that it is recommended to define in an associated protocol (refer to Appendix I for a recommended file naming convention). When filename standardization is not necessary, any name can be used as “Filename”. Choose “Create .map” in “File” of the menu bar and all positions, boundaries and references displayed in the camera feed will be saved in the .map file and a snapshot image “.jpg” of the camera feed will be saved in the same folder.
How does the "Clear Positions" function work?
Right-click of the mouse over the camera feed panel: This function removes all positions in the camera feed panel.
How does the "Sub-SurfaceID" function work?
This function allows the selection of a sub-surface and the edition of the Sub-SurfaceID name. When selected, the color of the position markers in camera feed corresponding to the selected sub-surface changes (from grey to black) in order to facilitate visualization.
How does the "Template Used" feature work?
This feature indicates which surface positioning template has been used to position the sample in the camera feed. When a surface positioning template is imported into the Mapping Toolbox through the function “Import.map”, this feature indicates the filename (*.map) of the last template imported.
How do I access the Help Menu?
The Help menu contains basic help functionalities (Figure 1) such as the user manual and information about the software/camera firmware.
User Manual - Click on this button to access a PDF file of this User Manual. The Adobe Reader™ must be installed on your computer. Visit https://www.adobe.com for installation details.
About - This function provides information about the software, firmware versions and camera serial number (Figure 2).
User Manual - Click on this button to access a PDF file of this User Manual. The Adobe Reader™ must be installed on your computer. Visit https://www.adobe.com for installation details.
About - This function provides information about the software, firmware versions and camera serial number (Figure 2).
How does the Camera Menu work?
The Camera menu provides the ability to control the camera feed.
Start - This function starts the camera feed. In this mode, the user can use all features in the Edit menu.
Stop - This function stops the camera feed. In this mode, the user cannot use all features in the Edit menu.
Start - This function starts the camera feed. In this mode, the user can use all features in the Edit menu.
Stop - This function stops the camera feed. In this mode, the user cannot use all features in the Edit menu.
How does the "Water Refraction (5% Compensation)" function work?
If required, this function applies a +5% scaling factor to the display of the positions, boundaries and references marks in the camera feed panel (this does not affect the pixel coordinates saved in the .map file). This feature is normally used to compensate for image distortion due to the presence of solution over the sample during manual characterization mapping of a biological sample. Note that the scaling is relative to the center of the grid.
How does the "Set Grid" function work?
This function will open a pop-up window to allow the user to configure the grid of snapping dots according to either an image-centered square configuration (size, in pixels, can be set from 10 to 200) or table configuration (# mcolumns and # rows can be set from 2 to 50, extended on the full image size).
How can I add boundaries to my sample in a mapping?
The "Boundary" function displays the boundaries of the surface (or its sub-surface), if defined, to facilitate the positioning of the sample or to see the boundaries when they are created.
"Add Boundary" allows the user to define the boundary of sub-surfaces of the sample. Click the camera feed panel over several points along sample boundary and a closed contour will be created. It is recommended to add boundary points in a clockwise or anti-clockwise order.
Right-click the mouse over the camera feed panel and select "Clear Boundaries" to remove all boundaries in the camera feed panel.
Note. It is important to edit/select a sub-surface in the Sub-SurfaceID field in order to assign a boundary to a sub-surface.
How does the "Position ID" function work?
This function displays a position number at the bottom right of each position marker. These labels are consecutive numbers starting from 1 for the first position added in each sub-surface.
How does the "Grid" function work?
This function displays a grid of snapping dots, in the camera feed panel, defined by the user. If no values for the grid have been previously defined by the user through the "Set Grid" feature, the software will automatically prompt the user through the "Set Grid" pop-up window. The snapping dots are overlaid on the camera feed panel to make it easier to line up positions added.
How can I dimension the top view image of my sample for the mappings?
This function allows the user to assign the metric coordinates of Reference 1 (red) and Reference 2 (blue). When Mach-1 metric coordinates are entered, ScanX(mm) and ScanY(mm) characterizations are calculated and exported in a ".map" file when created. This function is only applicable when Reference 1 (red) and Reference 2 (blue) markers are displayed in the camera feed panel and when all four fields are different from 0.
Click the camera feed panel on the second reference mark and a blue marker will appear. At each click, the blue marker will relocate.
Right-click the mouse over the camera feed panel and select "Clear References" to remove all references from the camera feed panel.
Click the camera feed panel on the first reference mark and a red marker will appear. At each click, the red marker will relocate.
How can I delete a position in the Mapping Toolbox?
The "Delete Position" function allows the user to delete a position that is not overlaid on a location of interest on the sample. Click the camera feed panel on a position marker to remove it. For faster results, click and hold down the left mouse button on position markers displayed in the camera feed panel and they will be removed on mouse-over until the user releases the left mouse button.
How does the "Add Position" function work?
Note. It is important to edit/select a sub-surface in the Sub-SurfaceID field in order to assign a position to a sub-surface.
This function allows the user to define a position of interest on the sample. Click the camera feed panel at each location of interest and a position marker will be added. When a snapping grid is displayed in the camera feed (grey dots), click and hold down the left mouse button in the camera feed panel and position markers will be added and be aligned to the snapping grid until the user releases the left mouse button.
Future measurements will be taken in the same order that position markers are added to the camera feed panel.
This function allows the user to define a position of interest on the sample. Click the camera feed panel at each location of interest and a position marker will be added. When a snapping grid is displayed in the camera feed (grey dots), click and hold down the left mouse button in the camera feed panel and position markers will be added and be aligned to the snapping grid until the user releases the left mouse button.
Future measurements will be taken in the same order that position markers are added to the camera feed panel.
How does the "Create .map" function work?
The "Create .map" function creates a ".map" file containing all positions, boundaries and references displayed in the camera feed panel as well as a snapshot image ".jpg" of the camera feed.
How does the "Import .map" function work?
This function imports all information contained in a ".map" file (positions, boundaries and references) into the camera feed panel.
How can I open a ".map" file?
First, use the "Open .map" function to open a ".map" file. Note that Mapping Toolbox will open only the referred files that are in the same folder as the opened file. A secondary panel, Mapping window, will appear where any characterization will be mapped and where controls can customize the mapping view.
The following commands are accessible through this secondary panel:
a. Characterization. Let the user choose which characterization will be overlaid on the image.
b. Sub-Surface. Let the user choose which sub-surface will be overlaid on the image. By default, all sub-surfaces are overlaid on the image.
c. Show boundary. If selected, boundaries of the selected characterization of the selected sub-surface will be overlaid on the image.
d. Show positions. If selected, positions of the selected characterization of the selected sub-surface will be overlaid on the image.
e. Positions size. Let the user define the size of the positions markers (circle diameter) that will be overlaid on the image.
f. Show positions ID. If selected, a position number at the bottom right of each position marker of the selected characterization of the selected sub-surface will be overlaid on the image.
g. Positions ID font size. Let the user define the font size of the position number (circle diameter) that will be overlaid on the image.
h. Show mapping. If selected, the mapping of the selected characterization of the selected sub-surface will be overlaid on the image.
i. Mapping transparency. Let the user define the transparency of the mapping that will be overlaid on the image. 0 being no transparency and 1 being 100% transparency.
j. Log-scale mapping. If selected, a natural logarithmic scale will be used to generate the mapping of the selected characterization of the selected sub-surface. If not selected, a linear scale will be used.
k. Mapping auto-scale. If selected, the maximal and minimal value of the scale will be automatically defined by the maximal and minimal value of the selected characterization of the selected sub-surface.
l. Maximal value. Let the user define the maximal value of the scale.
m. Minimal value. Let the user define the minimal value of the scale.
n. Show mapping triangles. If selected, the Delaunay triangles of the mapping that will be overlaid on the image. A Delaunay triangulation method is used to divide the selected sub-surface into a set of triangles to generate a color mapping.
o. Triangles borders width. Let the user define the border width of the triangles that will be overlaid on the image
p. Interpolate to boundary. If selected, a Kriging interpolation, which is essentially a weighted-distance interpolation of irregular spacing data points, will be used to obtain a complete mapping of the selected characterization of the selected sub-surface. The basic idea of a Kriging interpolation is to predict the value at a given point by computing a weighted average of the known values of the function in the neighborhood of the point.
q. Save Image. Save an image ".jpg" of the right panel display.
r. Save Scale. Save an image ".jpg" of the scale. Note that if transparency is used for the display of the mapping, it is suggested to modify the scale (using an image processing software) to display it with the same level of transparency over a uniform color representative of the sample average background.
The following commands are accessible through this secondary panel:
a. Characterization. Let the user choose which characterization will be overlaid on the image.
b. Sub-Surface. Let the user choose which sub-surface will be overlaid on the image. By default, all sub-surfaces are overlaid on the image.
c. Show boundary. If selected, boundaries of the selected characterization of the selected sub-surface will be overlaid on the image.
d. Show positions. If selected, positions of the selected characterization of the selected sub-surface will be overlaid on the image.
e. Positions size. Let the user define the size of the positions markers (circle diameter) that will be overlaid on the image.
f. Show positions ID. If selected, a position number at the bottom right of each position marker of the selected characterization of the selected sub-surface will be overlaid on the image.
g. Positions ID font size. Let the user define the font size of the position number (circle diameter) that will be overlaid on the image.
h. Show mapping. If selected, the mapping of the selected characterization of the selected sub-surface will be overlaid on the image.
i. Mapping transparency. Let the user define the transparency of the mapping that will be overlaid on the image. 0 being no transparency and 1 being 100% transparency.
j. Log-scale mapping. If selected, a natural logarithmic scale will be used to generate the mapping of the selected characterization of the selected sub-surface. If not selected, a linear scale will be used.
k. Mapping auto-scale. If selected, the maximal and minimal value of the scale will be automatically defined by the maximal and minimal value of the selected characterization of the selected sub-surface.
l. Maximal value. Let the user define the maximal value of the scale.
m. Minimal value. Let the user define the minimal value of the scale.
n. Show mapping triangles. If selected, the Delaunay triangles of the mapping that will be overlaid on the image. A Delaunay triangulation method is used to divide the selected sub-surface into a set of triangles to generate a color mapping.
o. Triangles borders width. Let the user define the border width of the triangles that will be overlaid on the image
p. Interpolate to boundary. If selected, a Kriging interpolation, which is essentially a weighted-distance interpolation of irregular spacing data points, will be used to obtain a complete mapping of the selected characterization of the selected sub-surface. The basic idea of a Kriging interpolation is to predict the value at a given point by computing a weighted average of the known values of the function in the neighborhood of the point.
q. Save Image. Save an image ".jpg" of the right panel display.
r. Save Scale. Save an image ".jpg" of the scale. Note that if transparency is used for the display of the mapping, it is suggested to modify the scale (using an image processing software) to display it with the same level of transparency over a uniform color representative of the sample average background.
What is the “.map” file format?
The “.map” file is a tab-delimited text file containing the results of various characterizations performed on a single sample surface. Each column of the file describes information and results for one particular type of characterization (referred to as “CharacterizationX(Units)”) with the format presented in the table.
A “.map” file generally contains several columns (or characterizations), each with the same number of rows. A blank “.map” file is always created at the start and contains five characterizations (under the category: “MAPPING”). Each row characterizes a point in the image, it provides its pixel coordinates, its name (ID), its type, to which sub-surface it is attached and the results of all characterizations performed (when PointType is 0).
A “.map” file generally contains several columns (or characterizations), each with the same number of rows. A blank “.map” file is always created at the start and contains five characterizations (under the category: “MAPPING”). Each row characterizes a point in the image, it provides its pixel coordinates, its name (ID), its type, to which sub-surface it is attached and the results of all characterizations performed (when PointType is 0).
Note that in order to be properly managed by the Mapping Toolbox software, all raw data and “.map” file describing characterizations of a single sample surface should be placed in a single folder named “Filename” (see naming convention below). Any name can be given to a “.map” file, but it is recommended to use the following convention:
- a “.map” file containing only “PixelX”, “PixelY”, “PointID”, “PointType” and “Sub-SurfaceID” is named “Filename.map”.
- a “.map” file also containing results from CharacterizationX(Units) is named “Filename-CharacterizationX.map”
- a “.map” file containing results from Characterization1(Units), Characterization2(Units) and … is named “Filename-Characterization1-Characterization2-….map”. Whenever possible, in order to reduce the filename length, the category of the characterization can be used to describe characterizations of the same category. For example, a “.map” file containing the characterizations ScanX(mm) and ScanY(mm) could be named “Filename-Indentation-Dimensions.map”.
Mapping Toolbox – Different types of points in the camera feed
What menu items are in the Mapping Toolbox camera feed window?
The camera feed window of the software displays:
a. Actions accessible in “File” of the menu bar:
a. Actions accessible in “File” of the menu bar:
• Open .map, Import .map, Create .map and Exit
b. Actions accessible in “Edit” of the menu bar:
• Add Position, Add Boundary, Delete Position, Delete Boundary, Reference 1 (red), Reference 2 (blue) and Calibration
c. Actions accessible in “View” of the menu bar:
• Grid, PositionID, Boundary, Set Grid and Water Refraction (5% Compensation)
• Start and Stop
e. Actions accessible in “Help” of the menu bar:
• User Manual and About
f. Template Used: Indicates which surface positioning template has been used to position the sample in the camera feed.
g. Sub-Surface ID: Allows the selection of a sub-surface and the editing of the Sub-SurfaceID name.
h. Actions accessible with a right-click of the mouse (over the camera feed panel):
• Clear Positions, Clear Boundaries and Clear References
b. Actions accessible in “Edit” of the menu bar:
• Add Position, Add Boundary, Delete Position, Delete Boundary, Reference 1 (red), Reference 2 (blue) and Calibration
c. Actions accessible in “View” of the menu bar:
• Grid, PositionID, Boundary, Set Grid and Water Refraction (5% Compensation)
• Start and Stop
e. Actions accessible in “Help” of the menu bar:
• User Manual and About
f. Template Used: Indicates which surface positioning template has been used to position the sample in the camera feed.
g. Sub-Surface ID: Allows the selection of a sub-surface and the editing of the Sub-SurfaceID name.
h. Actions accessible with a right-click of the mouse (over the camera feed panel):
• Clear Positions, Clear Boundaries and Clear References
How does the Scan function works?
This function moves the X and Y horizontal stages (or Theta torsion stage) to the next position on a predefined positions list. Contrary to the other functions, this function is directly linked to the repetition number of the sequence (see Repetitions in the Sequence section). For example, in order to displace the stages to every position included on the list, the number of repetition of the sequence should correspond to the position number on the list (calculated in the “# Position” field). When the sequence is executed, the Scan function will move the stage to the first position on the list. At the second repetition of the sequence, the function will move the stages to the second position, and so on. When the number of repetitions of a sequence exceeds the number of positions on the list, the function will reuse the same set of positions in loop. For example, if a positions list contains 5 positions and the sequence is repeated 10 times, the 5 positions will be visited twice. To minimize the risk of damage to the load cell, before each repetition of the Scan function, the Z-axis stage will first be repositioned to the position it was at the first Scan of the sequence.
Parameters:
POSITIONS X-Y (UNITS) - List containing the X and Y (or Theta) coordinates of predefined positions.
LOAD X-Y - Loads the X and Y (or Theta) coordinates from a file (tab-delimited text file). When prompted, choose the file that only contains the coordinates to be added to the list.
PASTE X-Y - Pastes the X and Y (or Theta) coordinates from the clipboard into the table.
CLEAR XY - Clears all the X and Y (or Theta) coordinates in the table.
Parameters:
POSITIONS X-Y (UNITS) - List containing the X and Y (or Theta) coordinates of predefined positions.
LOAD X-Y - Loads the X and Y (or Theta) coordinates from a file (tab-delimited text file). When prompted, choose the file that only contains the coordinates to be added to the list.
PASTE X-Y - Pastes the X and Y (or Theta) coordinates from the clipboard into the table.
CLEAR XY - Clears all the X and Y (or Theta) coordinates in the table.
Will you upgrade software from time to time? Do I need to pay for software upgrades?
Biomomentum Inc. warrants you that free software upgrades, when available, will be provided for a 24-month period from the date of shipment. After this time, upgrades will be provided, when available, at a separate charge, or under a separate agreement.