CONCH^© v. 1.0 software user manual

What is CONCH^©

Morphological analyses of ammonites are a time-consuming process. The software CONCH^© allows to gather the established sets of morphological characteristics (i.e., diameter, whorl height, whorl interspace, umbilical width) as well as the traditionally derived parameters and three different rib density parameters in steps of 10, 30 or 45 radial degrees (Hoffmann et al. 2015, Klug et al. 2015). Data can be exported as .csv files, images of the ammonites with set landmarks can be saved, and projects can be stored for later continuation.

The software thus streamlines ammonite analyses and allows scientists to converge on a single software to perform all ammonite morphological analyses for enhanced compatibility in the future.

System requirements

Software usage

The current version of CONCH^© calculates distances in images that have been scanned using a tabletop scanner. Images taken at varying magnifications (e.g., under the microscope) or via cameras are not yet supported, but this is planned for a future update. CONCH^© currently uses the resolution (dpi) of the image to automatically calculate distances. If the image resolution has been changed by the user, it is necessary to also change the image size alongside the resolution to avoid inaccurate measurements.

Example: The image has been scanned with a resolution of 300 dpi and has a size of 1200 × 1200 px. If the user increases the resolution of the image to 600 dpi, the image size must also be doubled to 2400 × 2400 px; otherwise the values returned by CONCH^© would be only 50% of the real values. Accordingly, if the resolution is reduced to 100 dpi the image size must be reduced as well to 400 × 400 px, and so on.

If all resolution and size values are correct, CONCH^© automatically returns all values in millimeters.

Measurement procedure

The graphical user interface is depicted in Fig. 1. The standard measurement procedure in CONCH^© is as follows:

1. Load an image in .jpg-, .tif- or .png-file format in the CONCH^© software via the Load image button. Note that it is not currently possible to rotate images in CONCH^©. The image must be rotated before in another graphics application, such that the oldest part of the conch is at the bottom (where the 0° grid marker will be).
2. Enter the specimen number in the popup dialogue. Default: the name of current image file.
3. Insert a measurement grid on the ammonite. Click any of the 10°, 30° or 45° buttons, all of which are available for clockwise and anti-clockwise coiling, and double-click in the center (protoconch) of the ammonite.
4. Place the M-markers on the image. Click the M button and place each marker via double-click. The M-markers are to be placed at the intersection of the exterior side of the shell and the measurement grid, in order of the grid starting at 0°. Right-clicking in the approximate region for the next marker starts the lens, to allow more precise placement. Note that M-markers, once set, cannot be deleted anymore, only replaced. Once all M-markers are placed click on Finnish marker placement to continue with the next step. Note that after the Finnish marker placement button has been clicked, no new M-markers can be set anymore.
5. If the image shows a heteromorph ammonite with whorl interspace, the WI-markers are then placed by clicking the WI button. They are, as the M-markers, placed in order of the measurement grid, starting at 0°, but on the interior side of the shell. Note that WI-markers, once set, cannot be deleted anymore, only replaced. The placement is finished by clicking the Finnish WI-marker placement button. Note that after the Finnish WI-marker placement button has been clicked, no new WI-markers can be set anymore.
6. After setting all markers, the rib values can be entered in the table. For this, highlight the row in the results table (on the right-hand side) which contains the marker for which the absolute rib index (ARI) is supposed to be measured. Right-click in the row and choose ARI40 and ARI20 for selected marker from the context menu. The area around the marker will be displayed in higher magnification, and circles with the right diameter for the ARI₂₀ and ARI₄₀ counting are displayed. Count the ribs and enter them in the table via the entry-dialog. Similarly, enter the entry-dialog for the ribs per demiwhorl (RDW) index by choosing RDW for selected marker from the context menu of the table row. All rows for which RDW and ARI₂₀/ARI₄₀ have been entered are marked in green.
7. The measurement values can be exported as .csv file via File → Export → conch data. Correspondingly, File → Save current image can be used to save the image file including all set markers for later reference. The Project menu allows to save the current project, or to load an earlier project. In projects, all measurements including the image are saved, and can later be manipulated exactly as with a newly opened image file.

CONCH^© is designed as a workflow-program. This means that particular tasks are only available after another task was performed. For instance, the button that allows to set M-markers is only active after a measurement grid was set. The program thus guides the user through the process, minimizing the chance for errors in the digitalization.

Fig. 1: Graphical user interface of the CONCH^© software. A: Menu band, enabling to save and load project files and to export results. B: Load image button to load an image into CONCH^© and name the project. C: Buttons to insert a measurement grid in 10°, 30° or 45° intervals, either clockwise or anti-clockwise. D: M button to start placement of M-markers. E: WI button to start placement of WI-markers. F: Angular measurement button to start measuring angles in the image. G: Information panel, showing the chosen name and resolution of the image and metadata concerning the project. H: Tabular panel, where in different tabs the gathered data are displayed and the view options and colors of various elements in the image can be changed. The buttons to end all marker placements are displayed in the lower part of this panel whenever applicable. The image area in the middle displays the measurement grid, radial degree information, already placed M- and WI-markers, ARI₂₀- and ARI₄₀-circles and the cardinal spline in different colors (labeled in the figure).

Relocating misplaced markers

After the marker placement has been finished, misplaced markers can be replaced (but never deleted). To do that, select the row containing the marker to replace in the results table on the right-hand side of the program window. Right-click the row and choose either replace selected marker or replace selected WI-marker from the context menu. Then, double-click on the correct position in the image to move this marker to its new position. All table values that are influenced by the replacement are automatically corrected.

Attention: To relocate a WI-marker you have to choose the row with the correct marker number, not the row with which the calculations would be performed. Example: If you want to replace the WI-marker no. 13, you choose the line where the marker number column shows 13, even though the whorl interspace would be calculated with WI21 and M13.

Angular measurements

To enable angular measurements, an image must be loaded and a measurement grid must be defined as explained above. Upon clicking the Angular measurement button the first time, CONCH^© creates a new tab on the right-hand side. The table contains 20 columns and 250 rows and can be edited freely. The reference point for all angular measurements is the coordinate origin. Angular measurements are started by clicking the Start button.

By clicking and holding the left mouse button, a rubber band between the coordinate origin and the mouse cursor is displayed. Once the desired point is reached with the cursor, the left mouse button is released to define the first line for the angular measurement, which is then displayed as blue line in the image. The second point needed for the measurement is set in an analog fashion, and the second line is displayed as a blue line. Alternatively, right-clicking in the image opens a lens, in which the points for angular measurements can be placed via double-click. The text box angle shows the measured angle with a maximum of three digits. Clicking on Copy/New copies the value into the table, clears the text-box and deletes the lines.

The process can be repeated for all desired angular measurements. Clicking the Finnish measurement button ends the angular measurements procedure. The Angular measurement button can be clicked more than once, to enter additional values into the table even after the Finnish measurement button was clicked before. Results can be exported as a .csv-file via File → Export → angles.

Customizing CONCH^©

CONCH^© offers limited customization options for the user.

Switching display of certain elements on or off

The tab view on the right-hand side allows to change the display options in the image. You can choose to switch display of the measurement grid, grid labels, M-markers, WI-markers and the image itself on or off. Likewise, you can switch on the display of all circles for the ARI₂₀/ARI₄₀ calculations, and a cardinal spline that runs through all markers can be displayed. The marker labels can be switched off for better visibility, and all marker crosses can be replaced with markers of 1 px size.

Changing colors and fonts

The tab colors on the right-hand side allows to modify the color of the following elements: Measurement grid, grid labels, M-markers, WI-markers, spline lines for angular measurements. The used font for the grid labels and markers can be changed as well.

Example data

We provided an example image (Example.tif) of an Aegocrioceras bicarinatum specimen from the clay pit Resse (Hoffmann et al. 2019) to load in CONCH^© and learn how to use the program. We further provide a project file (Example-Conch-Projectfile.Conchproject) where we placed all markers in the same specimen, to load directly in CONCH^© and see how a finalized measurement can look like.

Copyright notice

This program is released under the GNU General Public License (GNU GPLv3), available at https://www.gnu.org/licenses/gpl.txt.

Copyright 2017 René Hoffmann, Peter Goeddertz.

Cite as: Hoffmann, R., Weinkauf, M. F. G., Wiedenroth, K., Goeddertz, P., and De Baets, K. (2019) Morphological disparity and ontogeny of the endemic heteromorph ammonite genus Aegocrioceras (Early Cretaceous, Hauterivian, NW-Germany). Palaeogeography, Palaeoclimatology, Palaeoecology 520: 1–17.

References

• Hoffmann, R., Weinkauf, M. F. G., Wiedenroth, K., Goeddertz, P., and De Baets, K. (2019) Morphological disparity and ontogeny of the endemic heteromorph ammonite genus Aegocrioceras (Early Cretaceous, Hauterivian, NW-Germany). Palaeogeography, Palaeoclimatology, Palaeoecology 520: 1–17.
• Hoffmann, R., Reinhoff, D., and Lemanis, R. (2015) Non-invasive imaging techniques combined with morphometry: A case study from Spirula. Swiss Journal of Paleontology 134 (2): 207–216.
• Klug, Ch., Korn, D., Landman, N. H., Tanabe, K., De Baets, K., and Naglik, C. (2015) Describing ammonoid conchs. in: Klug, Ch., Korn, D., De Baets, K., Kruta, I., and Mapes, R. H. (eds) Ammonoid Paleobiology: From Anatomy to Ecology. Topics in Geobiology, (Springer: Dordrecht), pp. 3–24.