In this blog, I'm going to talk about geometric morphometrics and my software "Modan." Specifically, landmark-based morphometrics is the starting point. In this article, I will briefly describe the process, or workflow in morphometrics.
Typically, 2D landmark-based morphometrics begins with taking pictures of the specimens. After taking pictures, all the coordinates of the landmarks are digitized using softwares such as ImageJ or NIH Image. Digitized coordinates are stored in a text file in tps format. This is "data acquisition" part. 3D landmark-based morphometrics is not very different. It just involves different devices that can measure 3D coordinates and appropriate software instead of digital camera and digitizing software.
The second part is "data transformation" part. To perform statistical analysis, raw data acquired from specimens should be standardized. In most cases, if not all, this process involves translation, rotation and scaling, according to the superimposition methods the researcher have chosen. This transformation can be done by softwares such as CoordGen of IMP and stored as x1y1 format file. Sometimes, additional editing must be done to go to the next step. For example, to use the data in statistical packages, additional columns that describe some attribtes of specimen, or group of specimens should be inserted. This is very tedious job, and can be even painful if you're doing it over and over again.
The next part is statistical analysis. According to what kind of analysis you actually want to do, there is a wide variety of choices here. SPSS, SAS, R, some programs in IMP, and so on. Basically, you feed the transformed data into the program and execute specific commands to get the results, as tabulated numbers, bivariate graphs, or some more pretty stuffs.
Okay, that's a rough sketch of how we do morphometric analysis in general. However, if you think about the whole process, you may notice that more than a few softwares are involved in "each" step of the analysis. When I started to learn how to do morphometric analysis a few year ago, I had to consult the email that my advisor sent to me and think very hard to figure out what I should do, which program I should use at that moment. Even though I have considered myself a power user for many years, it was frustrating experience. Some of the programs are nice, some others are terrible to use, which means the overall process was terrible.
As a result, the user experience is inconsistent and very much fragmented. The ability to understand the results and contemplate on the meaning is often hindered by the difficulties throughout the process, and make the researcher glad that he/she got some results anyway. My former advisor once said, "this is the real world. You have to deal with it." Yes, that's right. But still, I think there should be some better way to deal with it.
And that's why I began writing my own program, Modan.
댓글 없음:
댓글 쓰기