5  Main Traits

The Main Traits analysis is the workhorse of MorFishJ as it performs a complete morphometric characterisation of fishes. It requires the user input to trace the outline of the body and pectoral fin, and to position some reference lines (Figure 5.1, Table 5.1) and landmark points. The coordinates of these lines and points allow to extract 22 morphometric measurements described in Figure 5.2 and Table 5.2.

Figure 5.1: Reference lines traced on fish images for main traits analysis (see Table 5.1 for descriptions)

Table 5.1: Description of reference lines traced on fish images for main traits analysis

Reference line	Description	User input
A	Vertical line at the narrowest point of the caudal peduncle	Yes
B	Horizontal line touching the highest edge of the body (excluding fins)	No
C	Horizontal line touching the lowest edge of the body (excluding fins)	No
D	Vertical line touching the most anterior tip of the body	No
E	Vertical line touching the most posterior tip of the caudal fin	No
F	Horizontal line touching the highest edge of the caudal fin	No
G	Horizontal line touching the lowest edge of the caudal fin	No
H	Vertical line at the base of the caudal fin (end of the vertebral column or posterior edge of the hypural plate). Parrotfishes (Labridae: Scarini) are an exception and the line should be placed between the last and second to last scale lying along the midline (FishBase)	Yes
I	Vertical line touching the posterior margin of the operculum	Yes
J	Horizontal line cutting the eye in halves	No1
K	Vertical line cutting the eye in halves	No
L	Vertical line at the pectoral fin insertion	Yes

 

(a) Linear measurements

 

 

(b) Surface areas

 

Figure 5.2: Morphometric parameters taken on fish images (see Table 5.2 for descriptions)

Table 5.2: Description of morphometric parameters taken on fish images

Code	Trait	Description	Reference
TL	Total length	Length from the most anterior point of the body (D) to the most posterior point (E) (excluding the caudal filaments)	FishBase
SL	Standard length	Length from most anterior point of the body (D) to the the base of the caudal fin (H)	FishBase
MBd	Maximum body depth	Body depth at the deepest part of the body (excluding fins). Measured as the vertical distance between B and C	Bellwood et al. (2014)
Hl	Head length	Horizontal distance from most anterior tip of the head (D) to the posterior margin of the operculum (I)	Barnett, Bellwood, and Hoey (2006)
Hd	Head depth	Head depth measured at the vertical of the orbit centroid along K	Villéger et al. (2010)
Ed	Eye diameter	Internal diameter of the orbit measured along J	Bellwood et al. (2014)
Eh	Eye position	Vertical distance from the orbit centroid (J × K) to the bottom of the body (K × C)	Toussaint et al. (2016)
Snl	Snout length	Horizontal distance from the anterior margin of the orbit to the tip of the snout (D)	Barnett, Bellwood, and Hoey (2006)
POC	Posterior of orbit centroid	Horizontal distance from the orbit centroid (J × K) to the posterior margin of the operculum (J × I)	Bellwood et al. (2014)
AO	Anterior of orbit	Horizontal distance from the anterior margin of the orbit to the anterior margin of the body along J (AO may be close, or equal to, zero in species with very anterior eyes)	Bellwood et al. (2014)
EMd	Eye-mouth distance	Distance between the orbit centroid (J × K) to the anterior tip of the premaxilla	Bellwood et al. (2014)
EMa	Eye-mouth angle	Angle between EMd and a horizontal line intersecting the tip of the premaxilla	Bellwood et al. (2014)
Mo	Oral gape position	Vertical distance from the tip of the premaxilla to the bottom of the body (C)	Toussaint et al. (2016)
Jl	Maxillary jaw length	Length from the tip of the premaxilla to the intersection between the maxilla and the mandible (i.e. the corner of the mouth)	Toussaint et al. (2016)
Bs	Body surface area	Area of a polygon drawn following the contour of the body excluding fins, and up to the narrowest point of the caudal peduncle	Bellwood et al. (2014)
CPd	Caudal peduncle depth	Measured at the narrowest point of the caudal peduncle along A	Villéger et al. (2010)
CFd	Caudal fin depth	Maximum depth of the caudal fin	Villéger et al. (2010)
CFs	Caudal fin surface area	Area of a polygon drawn following the contour of the caudal fin, with the anterior margin marked by a straight vertical line through the narrowest point of the caudal peduncle	Villéger et al. (2010)
PFs	Pectoral fin surface area	Area of a polygon drawn following the contour of the pectoral fin	Villéger et al. (2010)
PFl	Pectoral fin length	Length of the longest ray of the pectoral fin	Toussaint et al. (2016)
PFi	Pectoral fin position	Vertical distance from the upper insertion of the pectoral fin to the bottom of the body (C)	Toussaint et al. (2016)
PFb	Body depth at level of pectoral fin insertion	Body depth measured along L	Villéger et al. (2010)

5.1 Analysis

Once the steps described in Section 2.2 are completed the screen will be populated with a number of windows:

• the ImageJ/Fiji main window
• the MorFishJ GUI
• a fish image (this is a duplicate of the raw image to prevent any modification)
• the ROI manager
• the Image scale dialog

While the majority of the analysis is automated, there are a number of steps that require the user input:

1. If available, add a scale to the image as described in Chapter 3.

2. Adjust the image if necessary as described in Chapter 4.

3. Select the orientation of the fish (i.e., whether the fish is facing left or right) from a drop-down list. This step is important for the correct automatic placement of some reference lines and points.

4. Select the fish outline following the instruction in the dialog. Trace a polygon around the body and caudal fin, excluding the dorsal, pelvic, and anal fins as in the example below. Also avoid including any portion of pectoral fin protruding from the body area. Once the selection is completed it can be adjusted as needed.

Tip

The points that define the selection can be moved. To add a new point to the selection press Shift and click on an existing point. To remove one point press Alt and click on the point. See Polygon Selection Tool.

5. Position reference line A at the narrowest point of the caudal peduncle. After clicking OK several automatic steps will split the outline in two, the body area (Bs) and caudal fin area (CFs), and add reference lines B-G.

6. Position reference line H at the base of the caudal fin to mark the end of the standard length.

7. Position reference line I at the posterior margin of the operculum.

8. Trace an ellipse around the eye as in the example below (see Elliptical Selection Tool for specific instructions on how to use this tool). After clicking OK two new reference lines (J-K) are drawn perpendicular intersecting at the eye centroid.

9. Place a point at the insertion of the pectoral fin as in the example below.

After clicking OK reference line L appears passing through the selected point and 14 new traits are drawn and added to the ROI manager together with all reference lines.

Note

Update from v0.2.2.

In fish with very anterior eyes, or positioned on top of the head (e.g. Periophtalmus spp. and many other blennies), the anterior edge of the orbit may lie outside the body outline. In such cases AO = 0 and the ROI for AO is not saved.

10. Select the outline of the pectoral fin as in the example below. After clicking OK this is saved in the ROI manager as PFs.

11. Trace a line on the longest ray of the pectoral fin. After clicking OK this is saved in the ROI manager as PFl.

12. Place a point at the tip of the premaxilla (upper jaw) as in the example below. After clicking OK a new trait (Mo) is drawn and saved in the ROI manager.

13. Place a point at the corner of the mouth.

Important

The point should be placed at the intersection between the maxilla and the lower jaw (fish skull anatomy), not where the flesh of the upper and lower jaw meet! See the example below.

Correct

Incorrect

After clicking OK the last three traits are drawn and saved in the ROI manager.

The analysis of the image is completed. In case of single image analysis a window named Traits containing all the results appears. This can be saved by clicking on File -> Save As.... All ROIs in the ROI manager can also be saved as a zip file by clicking on More >>> -> Save.... In case of multiple image analysis a new row will be added to the results file, the ROIs are saved in their directory, where also the rotated or straightened images are saved as .jpg files. The current image is closed and the next is opened. Repeat steps 1-13 for all images.

5.2 Results

The results file/table contains one row for each image and 25 columns. The first column, image_id, is the name of the image without extension. The second column, px.cm, is the scale of the image in pixels/cm. This will be NA for images without scale. The columns 3-24 are the morphometric measurements described in Table 5.2. All linear measurements are in pixels and all areas in pixels². The angle EMa is in degrees. The last column, time, is the time spent to analyse the image (steps 1-13) in seconds.

Barnett, A., D. R. Bellwood, and A. S. Hoey. 2006. “Trophic Ecomorphology of Cardinalfish.” Marine Ecology Progress Series 322: 249–57. https://doi.org/10.3354/meps322249.

Bellwood, D. R., C. H. R. Goatley, S. J. Brandl, and O. Bellwood. 2014. “Fifty million years of herbivory on coral reefs: fossils, fish and functional innovations.” Proceedings of the Royal Society B: Biological Sciences 281 (1781): 20133046. https://doi.org/10.1098/rspb.2013.3046.

Toussaint, A., N. Charpin, S. Brosse, and S. Villéger. 2016. “Global Functional Diversity of Freshwater Fish Is Concentrated in the Neotropics While Functional Vulnerability Is Widespread.” Scientific Reports 6: 22125. https://doi.org/10.1038/srep22125.

Villéger, S., J. R. Miranda, D. F. Hernández, and D. Mouillot. 2010. “Contrasting Changes in Taxonomic Vs. Functional Diversity of Tropical Fish Communities After Habitat Degradation.” Ecological Applications 20 (6): 1512–22. https://doi.org/10.1890/09-1310.1.

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1. The user has to trace an ellipse around the eye and lines J and K will be automatically drawn from the coordinates of this selection.