Morphometric Analysis - Science topic

Thank you

From my view IdavLandmark is the better option

All the best for your work

In ArcGIS, you can determine the direction of a polyline feature by using the "Calculate Geometry Attributes" tool.

You may consider using the following software when you're ready to collect landmark point data to support your geometric morphometric analysis:

Which ever joint you decide to analyze, you may want to try using the joint primitive within the Checkpoint software below:

I am not familiar with this classification to comment, but the meaning of phase is not obvious to me from the diagram. Phase is not a term I remember being used in describing channels.

I think the classification developed by David Rosgen would be more helpful and descriptive. His classification has been reviewed and recommended by Luna Leopold and many field hydrologists have used the Rosgen classification as a descriptive and analysis tool.

Of course, there may be other river, stream and channel classifications, descriptions and possibly terms that have been developed, and applied. If it is a common term used in your region, then hopefully you can find applicable answers to its meaning.

Thankyou @Mainak choudhuri

You can use leaf area meter of LiCor for leaf blade width.. not sure if it would help with leaf base angle

You should be able to complete the analysis using RRPP (which can handle mixed models). The pairwise function in RRPP is more flexible than trajectory analysis because you use it after running the model to set up the pairwise comparisons that you want to do. You run the model, see if you have interesting interactions, and design the pairwise analyses to show you whether those are because of different magnitudes of directions of the response. I thought of the trajectory analysis because of the "shape" parameter which compares the shapes of the curves (of the response, over time), but there are many possibilities for designing analyses. You know that there are differences at the outset, but you can compare population means over the course of the treatment to find out if they increase/decrease of if the differences, over time, are in the same direction. So even if your design isn't optimal, there is a lot that you can do.

ArcHydro does all you need. But simply, Upstream Flowlength + Downstream Flowlength = Basin Length

You can distinguish the ridgelines by analyzing the flow direction and/or aspect map of the watershed.

Topographic Index ; I am sorry I know several indexes maybe you write the exact equation that you need.

It is necessary to define the parameters which are in your formula Ff=A/Lb² because in this form Ff is not dimensionless.

Usually, the following parameters are defined for the watershed:

1. Form factor: Watershed Area/(Watershed length)² = A/L², Value < 1

2. Shape factor Bs : (Watershed length)²/Watershed Area = L/A², Value > 1

3. Elongation ratio: Diameter of the circle of watershed area / Watershed length = 1.128A^0.5 /L, Value < or equal to 1.

4. Circulatory ratio: Watershed area/Area of the circle of watershed area = 12.57A/P², where P is the watershed perimeter, Value < or equal to 1

5. Compactness Coefficient: Watershed perimeter/perimeter of the circle of watershed area = 0.2821P/A^0.5, Value > or equal to 1.

Regards

Dear collegue .

Arc hydro in Arc GIS will be morehelpfull tool for your task.

That is a good question.

Depends on the software and whether you have mapped all of the dams or not. I've done something similar with culverts in order to "hydro condition" the DEM. If you have GIS software like ArcGIS or QGIS you can digitize small polygons on top of where the dam is. Then attribute those polygons with the elevation of the river below the dam. Convert the polygon to a raster with the same cell size as your original DEM. In ArcMap you can run the mosaic tool, add both the new rasters and the original DEM, and then set the preference for FIRST but making sure that the new rasters are on top in terms of the order that you enter them into the mosaic tool. The general approach can also be automated if you have a shapefile of dams and the locations are accurate.

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.

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 -

First need to determine in which stream order network delineation then based on the river order determine the threshold value.

I see that there is another scientific shortcut looming, purporting the well-known “philosopher´s stone” of geomorphology and basin analysis. It is similar to the approach taken in geochemistry where a plethora of indices and ratios pretend to avoid experience and knowledge in geology and mineralogy prior to the use of endless numerical datasets.

In the current issue there will be no by-pass of geoscientific anamnesis and visual examination (mapping, sampling leading to 2- and 3-D visualization as well as follow-up laboratory analysis.

Numerical analysis encompassing hydrography such as sinuosity of channel systems, slope angle must be supported by hydrodynamic investigations (GMS tool = granulometry, morphology, situmetry) all of which is grouped under the header “geoscientific measurements, analysis, and computations”. It needs to be corroborated by measurements in structural geology and by in-door analysis of the mineralogy, petrography and chemistry as well geochronology using methods appropriate for the Quaternary and Neogene , in particular. Any stand-alone synthetic geomorphometric analysis will yield synthetic results.

To substantiate my arguments I refer to the following papers dealing with this holistic approach in basin analysis and geomorphology.

DILL, H.G., BUZATU A., BALABAN S.-I. , UFER K., GÓMEZ TAPIAS J., BÎRGĂOANU D. and CRAMER T. (2020) The “badland trilogy” of the Desierto de la Tatacoa, Upper Magdalena Valley, Colombia, a result of geodynamics and climate: With a review of badland landscapes.- Catena 194: 1-20.

DILL, H.G., BUZATU A., BALABAN S.-I. , UFER K., TECHMER A. SCHEDLINSKY, W., and FÜSSL M., (2020) The transition of very coarse-grained meandering to straight fluvial drainage systems in a tectonized foreland-basement landscape during the Holocene (SE Germany) – A joint geomorphological-geological study.- Geomorphology (in print)

Available and ready for download on the RG server.

H.G.Dill

Dear Alejandra,

The eigenvectors are available in MorphoJ in tabular form in the text ouput. They are called 'PC coefficients'.

Best,

Dimitri

If you are good in Python/R there are couple of scripts available. If not, try ImageJ- depends on what depth of morphometry analysis you want to do. You can also use NucleusJ plugin in Image J. Check these paper-

Good Luck !!!

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.

I think it depends on your requirements. Each software comes with default parameters, but they can be adjusted to increase or decrease the number of streams. The topography is an important factor, flat areas do not require a dense drainage extraction.

You could try with GRASS GIS, see the documentation of r.stream.extract module.

Lizardo

Your welcome

regards

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")

Truss is a geometric protocol for character selection which largely overcomes the disadvantages of conventional data sets and it leads to certain style of analysis. In truss system, homologous landmarks on the boundary of the form are divided into two tiers and paired. The distance measures connect these landmarks into an over determinate truss network which is a series of quadrilaterals each having internal diagonals. Each quadrilateral shares one side with each succeeding and preceding quadrilaterals. Please following the link below:

Thanks Bader, your paper is particularly useful.

I used ImageJ, ZEN 2.5, and Imaris® for morphometric analysis of GFAP positive astrocytes.

Take a look:

If you are going to perform a large-scale analysis of 3D astrocyte morphology, I would strongly recommend Imaris. With this piece of software, you can reconstruct individual cells and analyze the number of astrocytic protoplasmic processes. The analysis of the stain intensity and cell volume can be done very easily in ZEN 2.5, which is much more powerful compared to ImageJ.

Good luck!

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.

Kenneth De Baets and it seems you miss my point too. These "classical measurements" cannot be implemented here. Even counting lobes, which seems trivial, cannot be objectively done as soon as the suture line is a bit complex. For example, tell me how many lobes do the 2 sutures with highest PC1 have? Where do you place the boundary between an indentation a bit stronger than the others on one lobe, and a subdivision of a lobe into 2 separate lobe? When does an indentation becomes a proper individualised lobe? My point (and in total disagreement with Dieter) is that these classical measurements or counting are not applicable here. They are easy to make with goniatitic and similar suture lines, but not in this case. These measurements will reflect more the observer's point of view than an actual morphological signal. one of the interests of geometric morphometry is exactly that, to provide an objective description of shape, independent from the observer.

Hi

for perimeter calculation you just right click on basin shapfile and then select attribute table and then create a field with a specific name. Then right click on this column and select calculate geometry tool. when you select this tool a window will appear that say which geometry you want to calculate. you should choose Perimeter and press Ok button. After this you can find the calculated perimeter..

For basin length calculation you need longest flow path and basin area. By dividing basin area per longest flow path, basin length can be obtained. For calculating longest flow path a suggest you GeoHMS or ArcHydro extensions. If you need more help, don't hesitate to contact me.

the best

Azizian

Thanks Aleks!

Hi Juniper,

From Mega, you can save your tree in newick format, which can then be read in programs such as FigTree that can export the tree(s) as a nexus file and including the tree annotations.

Best - Thierry

The justification for PCA is that, being just a rotation of the data, it preserves the Procrustes distances between points in the tangent space. Your plot thus shows the (main dimensions of) variation around the mean in units of Procrustes distance and your Procrustes Anova uses those distances when computing sums of squares. So you are depicting the variation in the same units that you use to quantify deviations from the mean in the statistical analysis. As far as I know, kernel PCA is used when the units are meaningless (or incommensurate across variables). 

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!

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.

Have you link of this books ?

It is not clear for which river basin. However, what you are asking is a processed information, which will not be available in public domain unless it is published by the analyzer. 

Prioritization of watershed for what purpose ? First of all you have to spell out what type of problem you want to solve, based on that one can guide what parameters you have to study; what approach you have to adopt and what should be your fixation of criteria for prioritization of any given watershed. 

R package missMDA

Thanks a lot Thomas

I'm running some clustering analysis with R. Quite difficult with so few material available, most of the times just one ant per sample.

Some patterns are emerging, though

I do not know if it includes reflection, I think you have to do this manually. But better check before doing all the work...

Best, Thomas

Have you tried using polarized light  filters?  

Dear Rahim,

I'm not sure how much this would influence the final results, but lens distortion from the camera itself might influence your landmark positioning as well if you took your photos with different zooms and angles. As long as you don't do image-stacking, your pictures will always have some slight distortion expecially towards the corners of the photo, which will obviously result in different distortions of the object you photograph with variable zoom and angle.

Does anybody know of a study assessing this possible technical error? Would be interesting to see how much that actually influences the landmarks...

Cheers,

Emanuel

Dear Aysha:

Your first picture belong to the genus Thalassiosira which processes has not external tubes, with a central fultoportula, a rimoportula on the valve surface at ca 11 hs and a marginal ring of fultoportulae. You need internal view of the valve and details of the morphometric data. Your material could belong to the group of T. oestrupii probably.

The other pictures correspond to the genus Actinocyclus, they show submarginal pseudonodula. You need internal views of the valves of the species.

See Tomas (1997) for seeing most important features of genera.

Kind regards.

Eugenia

Danilo:

This link may prove to be of some help:

Best

Syed

Dear Travis,

Maybe you will find this step-by-step ImageJ morphometrics tutorial useful:

All the best,

Eszter

Dear Colleague,

I suggest that you contact Dr. Paula Mabee (in RG).  She has worked intensively on this subject, especially on ontologies. See her list of publications.

Best wishes,

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

Dear Dominique Ponton,

I have sent my project to your email. 

Thanks

Rongrong Li

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.

Bogdan:

You may find this link useful:

Best

Syed

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

Hi Epa, you can use the draw background curve tool in tps.Dig (yellow pencil) to draw the curves and re-sampled the curve with a number of point which can append to landmarks using tps.util. 

Kind regards

Thank you sir, i will do with the help of advanced editing tools in Arc GIS as your mentioned above. 

In principle, it is possible to scale and translate landmark configurations (to remove variation in size and position), without rotating them. Of course, this requires an interpretable orientation of the studied objects and a common reference system.

Best,

Philipp

THank you dear Michael

I've made a test and found that the orientation of the source outline influences on the signs of NEFD coefficients.

On the attached images there is the same outline with two different orientation. Yellow segments indicate orientation. Bellow are NEFD corresponded to each case (starting from the 2nd harmonic). It is apparent that b_n and d_n change their sign.

Does obtained results mean that all compared outlines should be equally oriented?

Dear Anton:

I suggest you that you look at my Book Fourier Descriptors and their applications in Biology, Cambridge University Press (1997) for background and some case studies using elliptical Fourier analysis (EFA). Also, if you do an internet search you will find a large number of studies that have now used EFA. I hope this is useful for you. If you have any questions you can reach me at plestrel@earthlink.net.

Pete E. Lestrel, PhD

check this paper may be u will find it helpe you : C. Mengoni , N. Mucci, E. Randi, 2015 - Sex identification in four leporid species (Lepus corsicanus, Lepus europaeus, Lepus timidus and Lepus capensis mediterraneus)

I'm not familiar with RMorphand a cursory online search only brings up references to that book.

I've had success with the R Package Geomorph which may be of help to you; it's designed to handle general landmark geometric morphometrics in 2 and 3 dimensions.

Likely, and I have seem this many times, the DEM developed flat surfaces such as flood plains and terraces, and the flow accumulation tool does not know what to do, so you get straight lines in the direction of the flat slope (grade).  If you obtain LIDAR, you can generally get the stream connections right in modeling or by hand.  If you can see ground surfaces, you may not need LIDAR for this detail.  In wide heavily vegetated valleys, there is no way to predict fairly precise stream connection detail without LiDAR or ground surface surveys.  But as you see, the straight lines are just a remnant caused by how they predict water will flow across a relatively flat surface.  Some flow accumulation modelers have gone to raster with infinite flow directions instead of the normal 8 directions.  But sometimes the DEMs have these flat gradient areas, perhaps from filling sinks or ???  You may have manually go in and correct when streams flow through these flat areas.

See if you can access this thesis by Dr. Bennik at Auckland University... hope that helps

This is a problem that people have tried to solve when applying land marks to snail shells, which are almost just a continuous curve, so there are few places on can add fixed landmarks. One solution that I saw was to add a rectangle in a drawing package that touches the extreme edges of the stricture. The four points where the box contacts the structure become homologous locations where fixed landmarks can be added. The slider can be strategically placed between them.

Googleearth, DEM for morphometric analysis and GIS.

I have found this article about these topic, because I'am interested in farm animal 3D techniques, that's about filming, modelling. And when you have the modell 3D geomorph is close, as I think...

You are entirely correct in your analysis, in that cells grown over slides will tend to be flat and you will have the entire nucleus visualized, whereas tissue sections will have nuclei sections taken at random nuclear sites and orientation. Therefore tissue sections are not the appropriate sample to accurately measure things like cell or nuclear size. However if you are looking for large variations, ie. nuclei that are markedly increased or decreased in size compared to controls, then it might still work; if you measure enough nuclei, you can get beyond the noise inherent in size variation due to sectioning. But if what you are looking for is a subtle, minor difference, you may be out of luck.

Hola Daniel,

Look at this page: SB Morphometrics http://life.bio.sunysb.edu/morph/

by Prof. F. James Rohlf.

Excellent catalogue of software, bibliography, manuals....

Have fun!

Well, a problem is that the RV coefficient makes little sense for biological structures because it ignores spatial scale and the distribution of landmarks across a structure. 

You may wish to contact Dr. Richard Heck at U of Guelph in Canada.  He does a lot on soil texture, tomography, and such.

Consult any textbook of hematology or clinical chemistry and ask somebody who can guide you personally through the anatomy of granulocytes,lymphocytes and monocytes. You can not feel SAVE without personal feedback from an experienced person.

thanks

I am planning to use a Traditional Morphometric Analysis to determine the quantitative measurement of morphological parts. If I already get a morphometric data, is it applicable to undergo a phylogenetic analysis to determine the evolutionary relationship of a different cultivars of Cassava?

SRTM DEM is better for  Morphometric Analysis compare to ASTER 

maybe this reference also can help you:

Importance of Measurement of the Diameter of the Aorta during Peroperative Blood Flow Monitoring; 14th Annual International Conference of the IEEE Engineering in Medicine and Biology Society; p.2402 - 2403; DOI: 10.1109/IEMBS.1992.5761425.