Science topic

Morphometrics - Science topic

Morphometrics are topic devoted to the discussion of methods of quantification and analysis of biological form and shape and its applications to the study of evolution, ecomorphology, quantitative genetics, ontogeny, phylogenetics, anatomy, anthropology and etc.
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I need to do a morphometric analysis of a watershed using ARC GIS software. However I am unable to find the morphometric toolbox to perform the analysis. Please advice where can I get the tool box from??
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Thankyou @Mainak choudhuri
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I am working on my Tesis, and I need papers related with morphology and morphometry of cockroaches or any related insect (opthopteroids).
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thank you!
Best wishes
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I have 22 character data of different fish
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It depends on what your goal for the job is. If you have the morphometric data during the months, a comparison test can be done for a single species during the months of collection. However, I say and I repeat, it depends on your goal.
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Anyone have the protocol or method how to analyses various morphometric parameter (area, volume, volume of cristae and matrix, volume of inner and outer mitochondrial membrane) from mitochondria from Transmission electron microscope image by using imageJ.
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Hi, this article Cells | Free Full-Text | A Universal Approach to Analyzing Transmission Electron Microscopy with ImageJ | HTML (mdpi.com) is interesting in using ImageJ to measure mitochondrial morphology, you might want to give it a try, good luck,
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I am interested in determining fish morphometrics by TRUSS network. Now how can I extract length/measurements by PAST software amonglandmarks on fish generated by tpsDig2 software? Can you please guide/recommend me any document/ manual/ link to some tutorial.
Thank you i anticipation.
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Dear João Neves sent.
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Dear Researchers!
Greetings!
I want to compare stomatal morphometric characteristics of various species (same family members at altered environments). ANOVA one-way test was applied using SPSS to analyze the variance within and between species subjected to stomata morphometry data. Tukey post hoc statistical significance test was also employed. Further, I would like to perform 'Clustering and Similarity-distance analysis'. Please suggest the procedures and kindly let me know if there is any free version of the software available.
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See the attached screenshot for a great book available in the z-library. The R package cluster contains all the programs. Best wishes, David Booth
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I am looking for a detailed manual that one can follow as a self-teaching guide for measuring nematode morphometric parameters. Similar to architectural blueprints use in constructing buildings.
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Hunt, D.J., Palomares-Rius, J.E., Manzanilla-L´opez, R.H., 2018. Identification,
morphology and biology of plant parasitic nematodes. In: Sikora, R.A., Coyne, D.,
Hallmann, J., Patricia, T. (Eds.), Plant parasitic Nematodes in Subtropical and
Tropical Agriculture. CABI Publishing, Wallingford, UK, pp. 20–61.
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Hello all,
We are using the Inspire 2 drone/Zenmuse x7 camera to capture aerial videos of cetaceans. From these videos, we extract still images from which we then calculate the length and width of individual animals using a software that calculates morphometric measurements based on the pixel dimensions of the images, the lens focal length, and the height of the drone.
The videos are recorded at 5280x2160 resolution at an altitude of between 45-50 meters, using the DJI DL 50mm F2.8 LS ASPH lens, shutter speed 1/500, 29.97 fps. For some of our images, our pixel dimension appears to be 0.00445 mm/pixel, while in other images it is around 0.0034 mm/pixel (pixel dimensions calculated using a control object). This change in pixel dimension does not appear to be correlated with either the height or the tilt of the drone, and we have tried to camera in both auto-focus and manual-focus modes. We are not sure if this is an issue with the camera settings or a sign of a larger issue, but we would very much appreciate any suggestions as to what might be causing this problem!
Thank you all for your time.
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It depends on on a combination of factors, including the equipment (camera, lens, and filters), film used, altitude, camera angle, and weather conditions. However, There are six primary sources of aerial image distortion: terrain, camera tilts, film deformation, camera lens, atmospheric bending, and other camera errors. The terrain, and camera tilts sources of air are considered to be the major sources that contribute the most amount of error.
Kind Regards
Qamar Ul Islam
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To compare morphometric data of two or more bees.
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Specifically what kind of analysis you have in mind? You can use any kind of general morphometry software like MorphoJ (https://morphometrics.uk/MorphoJ_page.html) or R package like geomorph (https://cran.r-project.org/web/packages/geomorph/geomorph.pdf).
The measurements themselves can be done in a variety of ways (micrometric eyepiece, software like Digimizer, etc), and the analyses can be performed with any kind of statistical software.
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The parallel drainages are commonly observed over estuarine environments, flood plains and reservoirs of the area
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We also faced a similar problem in the Jhelum basin. In larger basins, you are very much right that natural drainage is not always available for stream burning. Further in our case, the pseudo drainage occurred in flat surfaces and over the lakes. For lakes, we had the lake polygon layer to burn. I think increasing the threshold is one of the viable options that does reduce such spurious drainage lines.
The solution lies in between the opinions provided by W. J. van Verseveld Richard Gloaguen Neelakantan Sajikumar
Thank you all for this wonderful knowledgeable discussion.
Regards
Gowhar Meraj
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Using TPS Series of Prof. James Rohlf for resolving problems related to morphology is a common technique in academia. I already used this series in previous successful works, however I do not remember how we can produce NTS files for Thin Plate Spline analysis. I appreciate any help from experts.
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Is there a certain point in the procedure where you are getting stuck? Or maybe an error message ?
I know you may have already tried these, but they were helpful to me when I got stuck with a similar problem -
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my project is Identification of family members (3Taxa),I did ANOVA test for a set of Morphometric,Metric and meristic measurement ,there is no significant difference,what suitable test in such case.
also I look for suitable test for qualitative trait.
Thanks in advance
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If ANOVA fails to signify stats correlation I think that the raw data sampling is defective . Plese repeat the data collection as per SOP .
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These days I start with a novel project of drone-based geomonitornig of valuable weathering landscape (earth pyramids/stone dolls). Our plan is to make drone-based inventarization of the geoforms as well as calculation of their morphometry but also the follow-up of any human impact or degradation of the site. We will produce aerial videos, but drone-based 3D model and orthophoto with high resolution ( of about 0.1 m).
However, I can't find something similar in the literature so far at least to compare the approaches or to have a new ideas.
Any help is very welcome to me!
Thank you!
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Dear Ivica, here a chapter regarding guly monitoring (geomorphic changes) based on HR DEMs: DOI:10.1016/B978-0-444-64177-9.00010-2, In book: Remote Sensing of Geomorphology
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Geometric morphometrics is now being applied for fish species using landmark-based truss network system with different computer software. Can this network system be applied to other animal's morphometry and craniometry?
Thank you in advance.
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Dear Muhammad
Yes, of course. This approach can be used for any stable shape such as skulls, insect wings, molluscs shells, leaves, etc.
Be aware that the truss network is not theoretically equivalent to geometric morphometrics.
Cheers,
Kiavash
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Analysing hydrologically corrected DEM avails an opportunity to calculate morphometric indices such as drainage basin density(DD) (which takes manual approach). Can not DD and others be extracted automatically?
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Watershed delineation for the Amazon sub-basin system using GTOPO30 DEM and a drainage network extracted from JERS SAR images
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Could anyone suggest any online sources (databases, dedicated websites, etc.) on insect morphometric characteristics, please? I'm particularly interested in insect mouthparts and tarsi measurements. Thank you! I appreciate your time and help! Alina
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I am currently doing microcomputer (mCT) tomography of beetles. The owners of these tomogrofofs have websites where you can find the morphological characteristics of the objects under study. If interested, I will post links to you
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How morphometric and morphotectonic parameters of drainage systems help us to find out complex structural features such as shear/suture zones?
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Dear colleague, Mechanical degradation related to brittle shear zones may lead to linear patterns of the drainage system due to morphoselection or passive control of an underlying shear zone.
But many other geological contacts may also lead to this situation (lithol. contacts, etc.). Also, local morphoclimatic environment controls how well imposed a shear zone might be in the landscape. For instance, an interplate structure with high slip rate such as the Alpine Fault in N Zealand exhibits a discrete linear imprint, whereas you can follow long-lived inactive shear zones in cratonic areas throghout hundreds of kms.
So I´ll look for rectilinear depressions, fault saddles, etc, as potential indicators of shears zones, but I doubt if you can isolate specific diagnostic morphologies.
Hope this helps. Best
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I would like to know the characteristics that differentiate between this two species, it is very confusing.
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No difference clinically. Manage symptomatically.
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SL gradient index = (change in elevation/change in length of river)*L(river length), how can we calculate the L values?
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The length of river (L) can be defined in two ways; 1) straight line from river head to mid of two point of measurement or 2) the slope of the length of river from head river to mod of two point of measurement.
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I am looking for literature about the effect of aquatic pollution on fish morphometrics. Kindly may you suggest me the relevant literature. Thank you.
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I think it depends on the type and the degree of pollution. Different results have been reported:
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Can we describe a new species of fish based on the examination of morphometric data, meristic characters and comparative materials without DNA barcoding?
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We exactly CANNOT identity new species based on barcoding! Barcoding data could have a signal for existing of a new species, it's true. Barcodind identifies some BINs, nobody known what is it, and they change all the times after adding new sequences. Regading these strange products as something species-like is clearly contradicting to the main approach declared in the Preambule to the International Code of Zoological Nomenclature created for STABILITY.
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Can we describe a new species of fish based on the examination of morphometric data, meristic characters and comparative materials without DNA barcoding?
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It may be desirable to have DNA with morphology when describing a new species, but it is not required. After all and for practicality, species are recognized morphologically, not by molecular analysis. On the other hand I would strongly recommend not to describe a new species on molecular data alone if they cannot be shown to also be defined by morphological data.
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I am using PAST software to apply on morphometrics of fish. Can anyone tell me can I remove size effect using PAST as there is option present "remove size from distances" with ''allometric vs standard" which as based on Elliott, 1995 formula. But the confusion is that as Elliott formula is based on standard length, while PAST doesn't demand to feed standard length given in data and directly modify the values.
If someone is using PAST, kindly guide me in this regard. Thank you in anticipation.
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Dear Muhammad:
Your'e welcome. Good luck in your research!
Best regards
Pablo.
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Suppose the prior group classification of specimens is group 1, and during the classification process through discriminant analysis, very few or almost zero of the specimen fall in group 1. What would be the decision process on those group 1 specimens?
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I am interested to determine the morphometric characters of fish using TRUSS network system. Can anyone please suggest me the software and theirs manual to make landmarks and determine the distance between them.
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Combination of softwares like tpsUtil, tpsDig, PAST are useful for landmark based TRUSS morphometrics. However, landmark based Geometric Morphometrics (GM) assess the shape and compare shape. Softwares for GM analysis are R package Geomorph, past and MorphoJ. Manuals of these softwares are easily available online.
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I have exactly the same question as the person who is asking in this link:
All I know is that the number of rows and columns in this matrix are double the number of landmarks because one of them (either rows or columns) represents the variables, that is, the x- and y- coordinates of the landmarks within the tps format. The main issue with interpreting this matrix would be figuring out how does R arrange the variables. I'm guessing this would be 1x, 1y, 2x, 2y, 3x, 3y,...
Also this does not explain why columns and rows are BOTH double the number of landmarks. I'm (again) guessing that columns are (maybe) representing variables, and rows are (maybe) representing a number of principal components arranged by variation percentage explained, set by default to be the same as variables.
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I would not try to interpret the pattern of loadings by reading the numbers. Instead, I would plot the results. The function returns the shapes at the extreme values for each PC, so you can use the plotRefToTarget function to show the difference between the two extremes (or you could show the change from the mean to an extreme. In this example, the shape data are coordinates of landmarks, in a 3D array, in a file called "niger.shape". This returns a plot of the scores and the changes along the first two PCs, from the shape with the minimum to the maximum score along each.
niger.gm<-gm.prcomp(niger.shape)
plot(niger.gm,pch=21,cex=1.5,bg="black")
plotRefToTarget(niger.gm$shapes$shapes.PC1$min,
niger.gm$shapes$shapes.PC1$max,method="vector")
title("PC1")
plotRefToTarget(niger.gm$shapes$shapes.PC2$min,
niger.gm$shapes$shapes.PC2$max,method="vector")
title("PC2")
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I'm trying to identify different rodent species from footprint tracks. The rodents run over 'ink' and then leave a trail of footprints on card. Due to various reasons, the back pads of their feet sometimes fail to leave marks on the paper, and this, therefore, results in missing landmarks. (I used TpsDig to create the landmarks). I've tried various software to analyse these landmarks, such as PAST and MorphJ, but both don't seem to deal with missing LMs very well. Can anyone shed some light on what approaches may be best to deal with this problem?
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To my knowledge neither PAST nor MorphoJ can estimate missing landmarks, in fact in theory MorphoJ does not allow the use of semilandmarks. From your question I understand you are using 2D landmarks obtained from 2D pictures using TPSDig. Thus, my recommendation is use two packages available in R which allow estimate missing landmarks. In the first one Geomorph there are two algorithms that can be used using the function estimate.missing:
The first approach (method="TPS") uses the thin-plate spline to interpolate landmarks on a reference specimen to estimate the locations of missing landmarks on a target specimen. Here, a reference specimen is obtained from the set of specimens for which all landmarks are present, Next, each incomplete specimen is aligned to the reference using the set of landmarks common to both. Finally, the thin-plate spline is used to estimate the locations of the missing landmarks in the target specimen (Gunz et al. 2009).
The second approach (method="Reg") is multivariate regression. Here each landmark with missing values is regressed on all other landmarks for the set of complete specimens, and the missing landmark values are then predicted by this linear regression model. Because the number of variables can exceed the number of specimens, the regression is implemented on scores along the first set of PLS axes for the complete and incomplete blocks of landmarks (see Gunz et al. 2009).
The second one named Morpho also uses two functions to estimate missing landmarks. The function fixLMmirror allow estimate missing landmarks from their bilateral counterparts and in the fixLMtps function the missing landmarks are estimated by deforming a sample average or a weighted estimate of the configurations most similar onto the deficient configuration. The deformation is performed by a Thin-plate-spline interpolation calculated by the available landmarks.
Please note that these methods have different requirements.
Both packages allow use files derived from TPSDig, thus you can use your files. These functions allow you read landmarks into R in Geomorph readland.tps and in Morpho readallTPS
I hope this helps!
Cheers,
Miguel
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Do you have some suggestions about how to apply DAPC (adegenet R package) analysis on the Geometry Morphometry dataset?
The dataset contains 12 morphometric points characterized by XY coordinates for each specimen.
Thnx
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Dear Jobst, thank you!
It seems like an inspiring study.
J.
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Dear Researchers Society, I prepare my master's thesis on the genus Mentha L. (Lamiaceae Lindl.). Could someone suggest me useful articles, publications and websites about representatives of this genus, descriptions of species, their morphometry, a list of confirmed taxa, identification keys and other information that you consider relevant. I thank You in advance.
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Please go through the following RG links and PDF attachments.
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My colleagues an I have found a very old Taxux tree in Crimean Mts. Can morphometric data of the trunk be useful for rather plausible inferring its age? Please help with advice!
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Andriy; Of course you can core a branch and it will give you only the age of the branch. You must be reluctant to core the trunk of the tree. If you are reluctant, why is that?
I've never seen a paper that had a method of reliably aging a standing tree without counting rings. It's a puzzle! Jim Des Lauriers
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Hi all,
Is there currently a data repository for species morphometrics data? If not, I would like to start one (open source of course).
Would this be something other researchers would be interested in contributing to or using in their own studies?
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I don't know there is one. I would like to participate if you decide to create one
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I am trying to get an overview of already existing morphometric measurements done on Gadus morhua. Does anyone know a place, where I might be able to find extensive morphometric data, i.e. with as many measurements as possible done on each individual (eg. lower jaw length, lower jaw with, eye diameter, etc.)
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You can find that data in the on-line book "Gadiformes" of A.N. Svetovidov. 1948. Fauna SSSR. Pisces. Vol. IX (4).
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I want to study tectonic controls on drainage systems in my study area, which has varying lithology. How can we say a change in morphometric indices (such as asymmetry factor or basin elongation ratio) is due to change in lithology or due to tectonic control? How can we relate the Hypsometric curve with tectonic activity?
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Well,
Streams High orders (5 and above) indicate that the streams run down streams in soft rocks or in steep areas such as floodplains.
  The intermediate orders (third and fourth) are found in areas with medium slope and their increasing number indicates the rigidity of the drainage rocks.
Low orders (first and second) are found in high-sloping rocky cliffs due to the speed of stream water. The first ranks are short in proportion to the rest.
The normal bifurcation rate in basins ranges between (3-5) and is a natural reflection of climatic, terrain and geological conditions.
Their values close to (3-5) are indicative of the similarity of the pond's climatic and structural properties.
  Any rise or fall of the ratio above the threshold is evidence of pond asymmetry and terrain.
It is evidence of normal anomalies in the pelvis or of tectonic activity in the basin area.
Regards
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I am trying to collect world-wide data on snake morphometrics (e.g. mass, SVL, TL, sex, etc.). Could all willing researchers who have snake morphometric data please contact me and send me your data in a .csv file.
I will compile the list of citations according to contributions, as well as any others who you suggest should be named in the citation of your data.
Thank you!!
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Tristan D. Schramer I haven't, but I will now! Thanks!
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Hello,
I am trying to investigate interspecific patterns of shape variation in a large clade of fishes and to do a preliminary test to see whether any of the variation in shape is related to a variety of categorical environmental variables. I have already done PCAs and CVAs at various points and have even done a PGLS (I think correctly). But I was most interested in PLS (or some such analysis), because it could give me a much more succinct (multivariate) view of the trends in shape with respect to multiple environmental factors (one figure!) than would a PCA (which would require many univariate graphs to get ideas of multivariate trends and therefore lots of eye-tiredness for pub readers...). pPLS would be even better because I could get at those trends after accounting for phylogeny, but I'm not sure it can be done with categorical variables in one block and I'm not sure that plsDA will do exactly what I'm looking for. Does anybody have any opinions about whether (and how) this type of analysis can(should) be done or have citations I can check out? The few examples I have found that used categorical data only had one factor they were working with in a PGLS and I'm thinking very few people especially in ecology are using plsDA anymore. Thanks in advance for any help!
Jessica
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Here are a couple of papers to look at for PGLS, one that introduces the method for shape data---if you've already done PGLS, this may not be very helpful, but the second one should be useful and the first is useful background reading for PGLS, in general. I don't know what you are questioning about your PGLS; there are lots of issues (conceptual and statistical) and some of those are addressed in the second of these papers. If it's just a matter of not knowing whether you ran the analysis correctly, then the first of these papers should clarify that.
Adams, D. C. 2014. A method for assessing phylogenetic least squares models for shape and other high-dimensional multivariate data. Evolution 9:2675-2688.
Adams, D. C. and M. L. Collyer. 2018. Phylogenetic ANOVA: Group-clade aggregation, biological challenges, and a refined permutation procedure. Evolution 72:1204-1215.
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Hello everybody,
I have a set of 25 morphometric variables (distance-based) of fish and 1 categorical variable (river) with 9 levels. I am trying to find out a way, that will allow me to identify which of morphometric parameters from the whole set are statistically significant among groups (rivers). I have tried to do a discriminant analysis, but there is no information about significance of characters, only the coefficients of discriminants. Can someone please give me an advice how to do it? Thank you very much. Peter
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Yes, it looks like a straightforward ANOVA question. A couple of further thoughts. You ask 'which of the 25 variables differ significantly' so you will need to account for colinearity and multiple testing, and more importantly to decide what you mean by 'significant'. I don't recommend fishing for a method that gives a p value, but rather that you decide what you want to know and find a method that answers that specific question. If the question is more general, i.e. whether the fish in the different rivers in in some way different, then you may want to try a more multivariate approach in which you consider all the variables together. I would probably use PERMANOVA (to get around the assumptions underpnning classical MANOVA) for testing, and something like SIMPER to understand which variables are contributing to observed differences.
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I want to work on using geometric morphometrics to inform the phylogenetic relationships of fishes and potentially provide insights on the morphological implications of lifestyle transitions over evolutionary time (e.g., benthic -> pelagic). What should I look out for in desired regions in terms of landmarking, as well using morphometrics data with an existing phylogeny?
Suggestions for added literature reading are welcome, as I am only starting with Adams et al. (2013), which also has good stuff.
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Before you get too far into the literature, I'd strongly recommend reading this critical evaluation of methods:
Adams, D. C. and M. L. Collyer. 2018. Multivariate phylogenetic comparative methods: Evaluations, comparisons, and recommendations. Systematic Biology 67:14-31.
It's main focus is on the methods for analyzing the evolutionary dynamics of shape (and it explains why not to use some of the methods used in Davis and Betancur-R). I would also wait on using the methods introduced by Catalano and Goloboff until you understand the theory underlying Procrustes-based geometric morphometrics thoroughly.
While you are learning the theory, you might look at the software for conducting the analyses to see what methods are now available and how to use them, as well as reading empirical studies that use them. The R package geomorph (by Adams, Collyer and Kaliontzopoulou) provides all those methods. The main method for analyzing the evolutionary relationships between ecology and morphology is phylogenetic generalized least squares (PGLS):
Adams, D. C. 2014. A method for assessing phylogenetic least squares models for shape and other high-dimensional mutlivariate data. Evolution 68:2675-2688, and
Adams, D. C. and M. L. Collyer. 2018b. Phylogenetic ANOVA: Group-clade aggregation, biological challenges, and a refined permutation procedure. Evolution 72:1204-1215.
There is a large empirical literature on the evolutionary relationship between ecology and shape, but much of it predates the methods that can analyze that relationship rigorously. However, those methods do now exist. At present, there are no generally accepted methods that incorporate shape data into phylogenetic analyses.
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Dear colleagues,
Does anyone know how tpsdig2 estimates missin landmarks? They have a tool rigt next to the landmark marker called "next landmark is missing", which allows you to "skip" missing landmarks, or at least insert a value in place of that landmark. Does anyone know how the program does this calculation?
Thanks in advance.
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Hi Rafaela. Actually as far I know, the tpsdig does not estimates missing landmarks. When you use the option "next landmark is missing", it computes "-1.00000 -1.00000" as coordinates of that missing landmark in your .tps file. Then, when you load your file in R (for example) you can use the function "estimate.missing" of the geomorph package. In that case, you can use two different approaches to estimate as described in the help function.
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I have tried to compare different morphometrical parameters for my study area derived from SRTM, ASTER, ALOS, CARTODEM with reference to morphometric parameters derived from Toposheets.
I wish to recommend which DEM gives accurate results with reference to SOI Toposheets?
I need a statistical basis to base my argument.
Which statistical test shall I do for my research?
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I do not know if you still are struggling with the same issue, here are some help. What are the critical parameters you wish to compare and extract from those DEMs? Elevation, slope, aspect, hydrology, ruggedness are just a few of them. The actual ground verification you will compare the DEMs with are from toposheets. How accurate are those toposheets. You can go with RMSE comparison, but you will need quite a lot of points strewn across your region of interest. You can dissect the slope to classes and look for the compliance of the data points falling in those slope classes independently. Look for the attached papers of mine, you will get the idea. Good luck.
  • DOI: 10.1080/01431161.2019.1585593
  • DOI: 10.1016/j.measurement.2018.12.101
  • DOI: 10.1007/s10661-018-6890-1
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I tried to use Morphologika to format my data, but even the sample data set won't work (a message pops up "error in data") and the new software, EVAN toolbox, costs money to use. I want to be able to look at vectors to examine sex differences in shape to determine the severity and directionality of the sex variation at each landmark. But whenever I attempt to do the compare vector analyses, it says that there isn't enough appropriate data to analyze. Does anyone have this problem? Maybe there's a better software that I can use to study vectors/angles? Any suggestions?
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The angle between the vectors is a measure of the difference in the directions of shape change. If the two vectors point in the same direction, the angle between them is zero. So (in geomorph) the statistical test determines whether that angle exceeds what would be expected by chance. There are two functions that perform the analysis in geomorph, depending on whether the vectors are trajectories between means or regression coefficients (slopes). The functions that did the analyses up until this most recent version of geomorph (3.10) are two of the major changes The function for comparing trajectories between means is trajectory.analysis, which is now in the RRPP package (but geomorph depends on RRPP so this is a minor change except in the manual and in the arguments for the function). The function that compares slopes is now procDlm used in conjunction with anova.lm.rrpp, and pairwise (in the previous version, you'd use trajectory.analysis and advanced.procD.lm) You can see examples of these analyses in the vignette for the newest version of geomorph.
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I need to identify marine fish eggs collected from Sri Lankan waters up to lowest possible taxanomic level by using morphometric and meristic characters. Please recommend any guide or research papers relevant to my search.
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I'm looking for a good authoritative source that walks me through methods for morphometrics.
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Thre are a number of methods and it depends on the type of species you want to study
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Hello,
I am dealing with linear measurements of limb bones, and I already have run a PCA to explore the dataset. If I want to extrapolate an ontogenetic growth trajectory, what is the best approach?
Thanks
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Jonathan Wagner thank you very much. You helped me a lot ! I think i got this. =)
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Dear researchers, I need your help!
Here I am attaching picture of tiny Oxynoemacheilus sp.
I was wondering how is it possible to count number of scales in Lateral line when fish has got such tiny scales.
BTW. I have tried to look in binocular but could not see anything :(
Thank you in advance,
Otherwise I am hopeless :(
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If, and it seems so, these analyzes are post-mortem, you can fix the fish and stain the scales or the pores. There is a variety of stains that you can use, protocols are fairly simple so that should not be a problem. In this way, you should be able to determine the scales number and position easier. Hope that helps.
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Combination of morphometric and colorimetric has been applied for feature extraction in detection algorithm. In noisy background, this CV technique facing wrong identification results as well as ML algorithm being developed to tackle pixels cluster into salient image regions.
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Some interesting reading about color matching vs mathematical projection and perceived color vs color sensation by following:
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I heard that this parameter (DBM) is well known from continuum mechanics and is usually used for the analysis of volume changes in flowing liquids or gases. I am seeking some theories of how does it apply for neuroimaging morphometry.
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hi,
I believe that typically DBM, or tensor-based morphometry, estimates how much deformation is needed to make a brain fit into a certain template (an average brain). This would indirectly return an atrophy value.
You can visit the SIENA's fslwiki page (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/SIENA) or the papers attached below:
best,
J
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I would like to analyse the shape of parotoid glands between two species by using landmarks. But because of assymetries between glands of an individual (i have observed assymetries in many of my samples) i m doubtful to try it. I am also inexperienced in this approach. So,could anyone inform me whether it is an appliable idea to analyse the shape of parotoid glands ?
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Christopher James Evelyn I am thinking about both of them but mainly focusing on the positional status. Thanks for advices, i got them.
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Dear friends,
I do have morphometric data of a species from twelve different rivers -the morphometric data includes 24 measurements. can any one suggest more suitable statistical methods to distinguish them morphometrically to identify the variations. Presently i am about use ordination techniques like clustering or nMDS.
Many thanks in advance.
Sileesh Mullasseri
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You could go "all out", although this would entail switching strategies: if you digitize standardized pictures of your species of interest, taking care to include those features which you hypothesize will differentiate them based upon geographic location, you could use the resulting coordinates (entire morphology) as the variables of your investigation, using Procrustes analysis and PCA. The resulting variables can be made amenable to multivariate statistics, or subjected to ordination techniques to see whether you can separate the (geographic) groups based upon morphology. Not a quick fix though...
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Population dynamics and Molecular characterization of genetic variants of fish fauna
I have added following objectives for above work as a part of my Ph.D. thesis
1. Morphometric measurements of fish samples
2. Study of Population dynamics of economically important fish population
3. Gut content analysis of fish samples for assessment of feeding overlap
4·Study of genetic variants of fish samples for probing any positive mutation if any
5·Physico-Chemical analysis of water samples from different sampling localities
Are these objectives sufficient to support my Ph.D. thesis or i have to add some more data ? Moreover kindly guide me that according to the objective, are these two themes (Population dynamics and Molecular Characterization) are correlating with each other or not?
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Unfortunately, till now I did not have a study in this field.
I use comments. Thanks
With the best wishes
Mr Rezaei Ahvanooei.
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I have added following objectives for above work as a part of my PhD. thesis
1. Morphometric measurements of fish samples
2. Study of Population dynamics of economically important fish population
3. Gut content analysis of fish samples for assessment of feeding overlap
4·Study of genetic variants of fish samples for probing any positive mutation if any
5 ·Physico-Chemical analysis of water samples from different sampling localities
Are these objectives sufficient to support my Ph.D. thesis or i have to add some more data ? Moreover kindly guide me that according to the objective, are these two themes (Population dynamics and Molecular Characterization) are correlating with each other or not?
Kindly must consider my question?
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Estimates of effective population sizes and, related to this, estimates of genetic variation within and amongst populations might be interesting. If you have enough markers you might also be able to estimate relatedness among fish and from this infer quantitative genetic parameters (e.g. h2). There are many possibilities! Good luck!
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Analysing morphology-habitat relationships in a montane plant species, I am thinking of using slope exposition (i.e., northern, southern slopes, etc.) as one of the habitat features, since a direct measuring of all the associated microclimatic factors appears problematic. I have plant samples from many sites within a montane area of ca. 1300 squared kilometres and for each site I have slope sexposition data (cardinal and inter-cardinal directions). I need to correlate this data with leaf morphometric anatomical/morphological traits.
I would be grateful if someone could also recommend some papers reporting relationships between plant growth/occurrence and slope exposition in mountains.
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Alternatively, you can break your directions into a north-south and an east-west aspect component.You require assignation of angles or compass directions in degrees. Depending on your study system, one of these slope aspect components might be of greatest interest (for example if working at a temperate latitude, most likely you would expect the degree of N-S orientation to matter more biologically, due to the difference in solar incidences). If you take the cos (angle) this will give you the N-S component as a numeric form ranging from 1 to -1, with 1 being N (0 or 360 degrees) and -1 being S (180), zero indicates a compete east or west exposition. The Sin(angle) is the E-W component, again ranging from 1 (East) to -1 (West). Then you can run correlations and linear regressions with your data.
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in Arc GIS it is possible to measure morphometric characteristics of a basin, but I face difficulty to compute the above parameters. How can I compute it? help help. Thank you.
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In Arc GIS you can calculate the length of the main stream and the perimeter/basin length. Yoe have to open the attribute table of the stream layer. click on the "Table Options" tab then select the "Add Field" option there. Then in the "Add Field" dialogue box u may provide the name, type (double) and precision and click "OK". then the name provide u can bee seen in the attribute table as a column.Then go to editor tool bar and click on editor and select "start editing" and select the stream layer that u are going to edit. Then again open the attribute table of the stream and right click on the new column heading u created. Select the Calculate geometry from the drop down list. Then u may calculate the length of the stream by units u select there. Then click OK button and u may see the actual length of the strem in the column u created. Do the same for the Basin length.
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Hi there, I am doing a zooarchaeological analysis in rodent bones. I have identified the taxons involved and group them in size groups (Big, medium and small). So, besides that, I need to take measures from my bone ensemble. What do I have to measure for each one of the different bone types? (Long bone, short, flat, irregular and besides, teeths). For example: In a femur, should I measure the size of the diafisis and also the whole bone? or what? I do not have clue at all above this
I would really appreciate any advice in this matter
Thank you for your time
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Hi,
I am not a zooarcheologist, so may be my answer would not fit your needs but it my help you.
Here is some interesting stuff to read/follow:
- you have to identify clearly to which taxon is your bones
- you have to know which methods or measurement techniques to use and its bias
- you have than to check it through the Virtual Zooarchaeology of the Arctic Project (VZAP) : http://vzap.iri.isu.edu/ViewPage.aspx?id=230, direct access to the project database is here: http://bones.iri.isu.edu/ (in the classification field you choose mammalian than rodentia)
- check these links/papers:
+ Animal Bone Specimens Preparation Method: http://www.nara.accu.or.jp/elearning/2011/animal.pdf
+ Integrating Zooarchaeology and Paleoethnobotany: A Consideration of Issues, Methods, and Cases (Springer) : http://www.springer.com/la/book/9781441909343
Best.
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The extensive literature on crocodilian morphometrics focuses either on cranial morphology or body size indicators such as Total Length (TL), Snout-Vent Length (SVL) and Body Mass (BM). So far I have found very few research dealing with relative limb proportions in living crocodilians (e.g., Ouboter, 1996; Farlow & Britton, 2000).
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Sure, I have all of those. Please check the direct message I sent you.
Apparently this elusive work has additional information on crocodilian proportions, but I have not been able to find it so far:
Junprasert, S. and Youngprapakorn, P. (1994) Head length proportion and predictable equation of Siamese crocodile’s body length at Samutprakan Crocodile Farm and Zoo. Journal of the Thai Association for Trade in Reptiles and Amphibians 1 (1), 45–46.
Jorge.
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I am interested in comparing the overall body and head size of free-ranging mammals from different geographic locations. Since they are free-ranging, touching them or taking measurements with tapes are not feasible all the time.
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Dear Debottam,
the software developed by Montani (2001) can be useful for your research. However you must take pictures from diffenrent angles.
Best,
Cristna
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i have to describe a gall midge (Diptera) and than compare morphometric characters of the same population at 1st and 2nd generation
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Elena
The sample size depends on the research question or objective:
If you want to describe a morphometric character in a follow-up study or in two generation of insects, you can calculate your sample size for a statistical estimation of a population parameter (generally, the mean), then you need to stablish the expected variability of the morphometric measure, the confidence level and the precision that you will do the estimation. This sample size will be the same for each generation of insects.
But if you want to compare the morphometric character in the same population in two stages or generations, then you will perform an hypothesis test for two independent populations, then you need to stablish the expected difference between the mean of the two populations and the expected variability about this mean, the significance level and the power expected of the statistical test.
Like you can see, the sample size is given by the morphometric measure that you want to evaluate, and for this calculus, the expected values can be estimated previously with a pilot study or experiment like Pieter said.
Never use a convenience selected sample size and try to apply then inferencial statistics (estimations or hypothesis tests), something will be going wrong.
Best regards
Federico
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Hi. I am developing a machine learning model to predict the diagnosis of a subject using his MRI data preprocessed using Voxel-based Morphometry. So, I have two groups of subjects (patients and control), and each person has a 3D volume with 128x128x128 voxels in MNI152 space.
The problem is that the groups have significantly different proportions of gender (verified using Chi-square proportion test). In another type of data, I would "regress out" (using a linear detrending algorithm) the effect of the non-imaging variable. However, I am not sure if this would make sense in this kind of data.
Is it make sense "regress out" the gender (or age and head size) from the intensity value of the voxel? What would be the best way to address the confounding effect of these non-imaging variables?
PS: I am using a deep neural network as the classifier.
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If the underlying algorithm was linear, 'regress-out' approach would be somewhat applicable, yet, since this is ML and deep-learning, linear decomposition doesn't really make sence - because, if the relationship between, say, age, and Morphometry metrics is not linear, your regression would basically corrupt the data, when without the regression the non-linar algorithm would probably identify the relationship quine nicely.
So why not just incorporate age into the model? Add another input into your model, and pass age into it. Same with gender and any other characteristic of the subjects. With deep learning it's reasonable to assume the model would make appropriate use of additional inputs, if given enough samples. But, well, the same goes for any ML algorithm
Since this incorporation is a bit different than, say, adding several more voxels, and carries a more 'modulation-like' sence, I would assume that the NN would require more layers/neurons to 'build' the underlying relationship. However I do not know the starting point so the structure used (or planned for use) may easily be enough already.
Significant between-group difference isn't perfect, but is not a deal breaker, in my opinion
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My current research is based on dental morphometrics, hence I need this ASUDAS plaques as reference to standardize my samples.  
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Thank you Michelle for the update.
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I mean a software which orient the objects to the most efficient shape and after that, analyse the distances between the poitns from the cloud points. 
I am working with bones and other small objects. 
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I do not really understand your question but maybe the following might help:
Co-registration of point clouds or meshes can be done with a free tool called CloudCompare: http://www.danielgm.net/cc/
Cloudcompare has an ICP (+ scaling) algorithm to co-register two 3D objects (meshes or point clouds) and you can choose from various algorithms to compute and visualise the differences between them.
Also, the free Meshlab can do point cloud comparison: http://www.meshlab.net/
Cheers, Geert
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Hello, I am currently working on a fish morphometrics project. We are attempting to perform a Between Groups PCA with our morphometrics data as is it considered more efficient than a regular PCA when assessing biological groups. Would appreciate if anyone could recommend me a software or package to perform this analysis. 
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In the case of geometric morphometrics, you can also use MorphoJ
doi: 10.1111/j.1755-0998.2010.02924.x.
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Dear colleagues
How can we call the diversity of morphometric forms of the seeds of a population [ ex; of argan tree ] situated in the homogeneous ecological and climatic conditions?
Best regards,
Réda Kechairi
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I would refer to them as morphotypes. It is not unusual to find different morphs within seeds of the same species - what is interesting is why? When you say different forms, are you refering to size, shape?  
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I am working on Insects (Micro-hymenopterans) and trying to differentiate the two species of the same genus using morphometric as a tool. I found that Geometric Morphometric could be used for the objective proposed. So where can I learn this tool.
Please help in this regard.
Thanks in Advance.
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In addition to MorphoJ, you could also use PAST for analysis. It has several tools for morphometrics analysis and it is easy to use, just like MorphoJ. The other thing is you could just enroll for one of Klingenberg's GMM courses. He wrote the MorphoJ software plus he is an excellent teacher!
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I have done morphometric analysis of watershed ,which gives bifurcation ratio as 4.57, elongation ratio is 0.57,shows that this watershed is elongated and peak flow is extended .(it will come early?)
means,if normal watershed what ever peak flow occur ,in elongated watershed ,the peak flow is some what in later stage
is it so!
is anyone has books related to river morphometry(specially for drainage of river is concern),I have refered but few things came across!
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I agree with the answers of both Dr. William and Dr. Kevin. Considering all the other parameters being the same, it is quite a general rule that the occurrence of  flash floods is more in circular watersheds and there is extended time for the peak discharge in the elongated watersheds. There are class books written by the greats like Horton, Strahler and Schumm.
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The calcaneo-cuboid joint is formed by cuboidal articular facet of calcaneus and the calcaneal facet of cuboid.
Planning to do a morphometric study on cuboidal articular facet of calcaneus?
Not found any literature for this study.
So, kindly give your valuable views regarding the same.
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I agree with Sedat on the articles.  In my opinion the size means very little clinically 
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I've collected a diverse range of measurements from Painted Dogs and would like to calculate body condition.  Is there a general consensus using say weight/pes for large carnivores? Or weight and other landmarks. Is log or a natural log applied to respective variables? If you have a reference that I could follow up also that would be great. Thanks
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These two articles study baboons in the wild and have a measurement for body condition that they use:
Strum, SC (2005). Measuring success in primate translocation: A baboon case study. Am. J. Primatol., 65: 117–140. doi:10.1002/ajp.20103
Silk JB, Strum SC (2010). Maternal Condition Does Not Influence Birth Sex Ratios in Anubis Baboons (Papio anubis). PLoS ONE 5(9): e12750. doi:10.1371/journal.pone.0012750
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when a digenean specimens (belongs to the same species) isolated from different hosts, some morphological and morphometric changes occur. what are these changes?
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Dear Yassar,
Your questions can only be addressed/answered AFTER a morphological statistics investigation. Procrustes analysis is the method of choice. However, you will need to define landmarks and measure their coordinates (preferably in 3D). If you look at Warp Analysis, etc. you will get a signal as to which regions (defined by your landmarks) will be variable within a species (and therefore: which will not be).
Kind Regards, Hermann
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If so, which measurements of the rhamphotheca should be taken?
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Hello Virginie Plot 
please check the attachment
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Can anyone help me to get a a computer program used in the study of phenotypic characteristics of the insects. I would be grateful to him.
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There is a lot of free software for morphometric analyses.  Some programs are more useful for analyzing size measurements, others for shape. Some are point-and-click programs, others are packages for morphometrics that run in R; R gives you much greater flexibility and it is far easier to repeat the same kind of analysis many times, as well as to keep a complete record of what you did, but it does take time to learn enough about R before it is easy to use. I have written a general overview of free software for geometric morphometrics, but it is seriously outdated in the sections on doing morphometrics in R (it can be downloaded from ResearchGate). If you want to use measurements of size instead, you could do your analyses in R anyway, but as mentioned above, PAST is a reasonable alternative. It does the standard analyses and it is not that difficult to learn. If you plan to analyze shape, I would strongly recommend doing your analyses in R because the most comprehensive program for shape analysis is the R package geomorph. It has an excellent manual and a very complete Users Guide. It is also excellent for graphics. The first step in any morphometric analysis is collecting the data, and the tps program, tpsDig remains my favorite for that (it is for collecting data from photographs by clicking on landmarks and outlining curves). I've digitizing several thousand photographs using it and although I've experimented with other programs I have not found one as easy to use or as complete. That one you can get at www.life.bio.sunysb.edu/morph/. That is the Stony Brook morphometrics website and it has links to many programs (just follow the link to software). 
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I need to identify the type of fish caught from fish images. How can I locate anchor points/landmark points to extract features from the image?
Namely, I want to locate eye position, dorsal and pelvic fin. Need to get Fish mouth length, Dorsal and Caudal fin length.
Right now I am trying with SIFT method to get key points.
Can someone suggest me how can I get the specific key points?
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As mentioned earlier, the TPS software suite very useful and user-friendly in placing landmarks and performing basic analyses. http://life.bio.sunysb.edu/morph/
My former adviser has also worked on computer-based species identification. This may be of interest to you.
Best of luck with your work
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Dear all,
I am working on morphometry of a beetle community (cca. 30 species) belonging to three distinct families, but some of them clearly showing same way of life. We would like to detect which of 25+ morphological characters (mostly lenghts of different body parts, including legs) can be attributed to convergent evolution (i.e. in species belonging to different families but showing same way of life), and divergences (i.e. in species belonging to the same family but evolved differently, accordingly to their different ways of life).
Is there any explicit test for showing that? Is this possible to test without molecular data? (we know there are three distinct molecular groups, but we do not have our own molecular data)
I would be very happy to receive suggestions of any kind.
All the best,
Jure
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I just found a study of leporid lagomorphs that tackles a similar problem and uses 3D landmarks for morphometrics and phylo-morphospace plots:
Kraatz B, Sherratt E. 2016. Evolutionary morphology of the rabbit skull. PeerJ 4:e2453 https://doi.org/10.7717/peerj.2453
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when I use the "Residuals/Predicted Values From Other Regression" function in MorphoJ, I can't found the independent variables "data matric" and "variables"in the drop-down menus. Is there something wrong during my opretion? Thanks
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Dear Dominique Ponton,
I have sent my project to your email. 
Thanks
Rongrong Li
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I am using the first principal component of morphometric data as a response variable in a PGLS analysis. Log transformation of this variable produces residuals which have a better fit. Are there any issues with transforming principal component scores? 
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Hi Timothy,
You can take the log of your variable, there is no problem about it, and compute a common linear analysis. However, the beta-coefficients you will find using OLS method will be optimal for the regression log(Y) = X.beta + Epsilon (understand : they will minimize the sum of the residuals of the regression log(Y) = X.beta + Epsilon) but will not be the coefficients that will minimize the difference between Y and exp(X.beta).
However, it might be interesting to study the log(Y) = X.beta + Epsilon regression, but using numerical optimization (see Newton-Raphson algorithm).
Best regards,
Geoffrey
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I am using 2 curves with 15 evenly-spaced semilandmarks to capture the lateral morphology of a very disparate sample of bird beaks. The 2 curves are constraining by 3 regular lndmks forming a triangle, the tip-of-the-beak one constrains both curves. When I slide the smlndmks in tpsRelw with min-dsquare slide method most of the smlndmks collapse in a very narrow section of both 2 curves in the Procrustes superimposition. Minimum bending energy slide method does not affect the superimposition in this way, but I need to use min-dsquare.  Any idea what is going on here? Is it a bug of the program or is a proper statistical effect?
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You could subdivide the data set, use a subset of the landmarks or use statistical methods to analyze the data in shape space without projecting them onto the tangent space.
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I am new in this concept. So kindly provide some concept papers, analytical papers etc.
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Dear Sony,
If you are new to geometric morphometrics, I suggest you to first read some general papers such as:
and
A very good book to start with is "Geometric Morphometrics for Biologists: A Primer" (see the review at http://life.bio.sunysb.edu/morph/books/macleod_review_2005.pdf)
And a very good (free) software is MorphoJ (http://www.flywings.org.uk/morphoj_page.htm) or the geomorph R Package (https://cran.r-project.org/web/packages/geomorph/index.html)
Have fun (may be not at the very beginning ;-)
Best regards
Dom
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I am an MSc student and for my final thesis project I had set out to perform a comparative morphometric analysis between three avian families. My own dataset of one family returned results, however the dataset I was sent to perform the comparison with is unusable (none of us can work out why or how to fix this). Sadly, I do not have time to repeat any procedure and am having to settle with extremely restricted, unoriginal results. I have PCA results for all datasets, but as I am unable to run the datasets together, I cannot directly compare them.
I am struggling to write my report as no direct comparison between the groups was possible and as such I have no overall results. Is there a 'way' I can still write a decent report?
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Dear Roseanne,
If I am understanding you correctly the data that you have collected yourself plus the others from other workers are the subject of your Master thesis. For some reasons you were asked to do the comparison of three data sets: your own plus other two of other people. You write that the other two data set are not useful at all. Thus, I would suggest that you check the goals of your thesis, that are the foundation of what you are doing, and revise why you were asked for this work. It is not just to say that the other two data sets are not useful, because it is your duty to explain your reasons for saying this. It could be the case that they are not useful, but in sciences it is not just to say that others are wrong; you have to demonstrate that the data from others are wrong! You say that you do not have time now to run new analyses of those two data sets, but this is your problem not a problem of the comparative study that you were asked to perform.  My best suggestion is that you talk to your main advisor as soon as possible, and if it is needed, organize a meeting with your graduate committee about the problem that you have in hands. I strongly suggest to do this, other way you put your thesis in a risky situation.
With my best wishes,
Gloria Arratia
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We have a set of facial profiles - from the glabella between the eyebrows to the gnathion on the chin.
To me, it seems the most sensible way to decompose this shape into a Fourier series, would be to consider it as a single wave and use a standard Fourier decomposition.
I have noted, however, that most people facing the same problem will use an elliptical Fourier analysis, for the analysis of closed contours. In order to do this they will artificially make the surface closed e.g. by reflecting the profile and decomposing the two joined mirror images such as in Rose et al (2003) Lateral facial soft-tissue prediction model: Analysis using Fourier shape descriptors and traditional cephalometric methods. Am J. Phys. Anthropol. This is not the only paper to do this or something similar.
My question is: when the profile is simply an open line, why go to such lengths to use an elliptical Fourier decomposition, when the "regular" Fourier decomposition would serve the purpose? Or am I wrong that one could the "regular" Fourier decomposition in such a context?
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Consider say just a simple arc to represent a smile. Then following comes into play:
1. 1d analysis using FT or FS requires a defining ground line on x axis.
2 Suppose it is rotated 90 deg then we get a different FS (along x axis
3 Location in x y plane is to be synched.
In case of 2d shape , by reflecting to form a shape we overcome this difficulty. In other words we can  possibly be independent of camera orientation . Also topologically if the same person has a" wry" smile still we could say it is the mouth of the figure.
Cheers