Monday, March 31, 2008

Image Your World With ImageJ

ImageJ is probably one of the most universally-useful, open source programs available for scientists. This is a program designed for image analysis, whether you want to count points, generate an "x-ray" image from CT scan data, calculate moments of area, or measure the length and area of a feature on a photograph.

The "J" in ImageJ stands for "Java" - that platform-independent programming language. This means that you can run ImageJ on virtually any operating system. If you don't have a Java virtual machine installed (and most every system comes with one - if you don't have it, you'll find out when you can't run ImageJ!), the program's website allows you to download a copy with your installation of ImageJ. The only potential downside of running under Java is a small sacrifice in program performance in some situations.

Why Use ImageJ?
The real power of ImageJ lies in its extendability and its updatability. Updates are released for the program every week or two - these usually aren't just bug fixes, but real interface and functional improvements. Furthermore, there are scads of plug-ins and macros available. Want to import DICOM stacks more efficiently? Use a plug-in! Want to measure second moments of area? There's a macro for that! Can't find a macro to do what you want? Write one of your own!

I use two main features in ImageJ: the measurement tools and the stack tools. The measurement tools allow me to measure distances, areas, and other parameters, and I can calibrate these using a scale bar from within the photo. The stack tools are also quite handy for working with CT scan data. I use them to reslice my images in various orientations (say I have a coronal series, and want to look at another view) or to generate quick 3D volume renderings. Other programs (e.g., 3D Slicer) are better for dedicated CT work, but ImageJ is fantastic for quick-and-dirty CT data manipulation. Furthermore, the interface is simple and relatively easy to navigate.

Commercial Alternatives
Probably the closest commercial equivalent to ImageJ is SigmaScan. I used this program a few years back, so I can make at least a superficial comparison. As far as I can tell, the primary benefit of SigmaScan over ImageJ is that the former allows you to save the tracings you've made for area measurements (at least, this is a feature I found handy). A dedicated user would know other unique features, but then again ImageJ doesn't cost nearly $1,000 on academic discount.

Minor Drawbacks
There are a few limitations to ImageJ of which users should be aware. If you're going to deal with large stacks of images (such as a CT scan), you may bump up against problems in the default memory configuration for the program. Fortunately, this is usually resolved by a simple tweak of the initialization file. Also, it is important to remember that ImageJ is for image analysis, not image editing. A few tools within ImageJ (paintbrush, paint bucket, etc.) can help in this regard, but you're really better off going to GIMP for most image editing tasks. And, as mentioned above, you can't directly save and reload any selection boundaries that you might make for measuring area (if you want to remeasure the same area later).

The Bottom Line
All in all, if you measure images or work with CT slices, you want ImageJ on your computer.

Note: I forgot to mention in my initial post two other popular options - NIH Image and Scion Image, available for Mac and Windows, respectively. They have both largely been superseded by ImageJ (and were really precursors to it), but I just want to be complete.

Friday, March 28, 2008 2.4 released

It's been a great week for open source software updates! The new version (2.4) of is now available for general download. is a full-function office suite (Microsoft Office would be its commercial equivalent), which I've been using pretty much exclusively for the past year. I'll probably cover that experience in a future post.

The new version is what would probably be termed a "minor release," based on my few minutes of use (and a quick glance at the release notes). The user interface looks pretty much the same as other releases in the 2.x series, so users of the old versions won't have that tough of a time making the switch. The developers have tweaked in a few useful features here and there, such as drag-and-drop support in Calc (=Excel), some extra chart formatting options (e.g., adding the regression equation to a regression line), and a few other items.

For users of Ubuntu, a nice set of instructions on updating your version of are posted here (although you'll have to make an adjustment or two to account for the new version).

Tuesday, March 25, 2008

Inkscape 0.46 released

As if in response to my previous post, Inkscape 0.46 is now available for download. This version includes some handy new features, including:

-PDF import and export. (However, recall from my previous post that PDF doesn't always play well with transparency or clipping)
-Ability to import Adobe Illustrator files from 9.0 and later.
-Dialog boxes that can be docked along the work area. The convenience of this will be most apparent for people who have used previous versions of Inkscape. No longer will you be cluttered with annoying windows that you have to move around to avoid obscuring your drawings!
-A new "paint bucket" tool, that creates new, color-filled objects that conform to the shape of an object you select.

So far, official release versions are available for OS X and Ubuntu Gutsy. Windows, Fedora, and other versions are supposed to be forthcoming (and interested users could certainly locate a pre-release version).

Saturday, March 22, 2008

Inking It Up with Inkscape

A scientist does not live by photos alone. Often, it's nice to to include a little diagram, or line drawing, or composited photo collage, in your paper. In the world of commercial software, there are some really nice options out there, such as Adobe Illustrator and CorelDraw. Among open source problems, however, Inkscape takes the cake.

Inkscape is a vector illustrator - this means that rather than dealing with images as a set of pixels, it uses mathematical formulas to describe the curves, lines, text, and shapes that form the image. Thus, like Illustrator or Corel Draw, it's not intended for photos by themselves (see my previous post on GIMP for that flavor of software).

I have prepared a number of illustrations using Inkscape and have been immensely pleased so far. The user interface is pretty intuitive, and I can do most everything I want to do in preparing illustrations for publication. The image at right is one of the first diagrams I created with this program - any crudeness in the rendering is my fault, not Inkscape's! As you can see, it's easy to integrate lettering, shading, and line drawings or photos. Unlike some other open source programs, documentation for Inkscape is actually pretty good, too. There are even some handy tutorials at the program's Wiki page. Inkscape is under very active development (currently in versions 0.45.1, with 0.46 arriving soon), and is available in versions for Linux, Windows, and Mac.

Is Inkscape For You?
So, who would benefit most from Inkscape? I strongly recommend it for the average paleontologist, who needs to make figures for a few publications a year, or presentations, or whatever. The features are more than sufficient to do what you need to do (and you can't beat the [free] price tag!). Professional artists, or people who are married to Illustrator, may find it hard to make the switch to Inkscape. For instance, it's pretty much impossible at present to do color separations (as near as I can tell), which is a bit of a problem for those who need to regularly turn color into a printed copy. Those who primarily do their graphics for the web, though, will probably be in pretty good shape.

A Few Small Issues
The one area where I have been a little disappointed by Inkscape is in import and export. If you have files from a previous program, you may run into some problems. Inkscape only imports Illustrator back to version 8.0 (although see the notation below), and you're out of luck with importing directly from CorelDraw, DXF, or EPS (although you certainly can import indirectly via other formats). The only bitmap export format Inkscape does is PNG - it's not a problem, so much as an annoyance. You can always use another program to convert the PNG to JPEG, TIFF, or whatever other format you want. As for other export formats, Inkscape will do PDF, EPS, PS, and a few others. EPS is probably the most critical, because publishers often want their image files in this format. Yet, when I've had embedded images, I've also found that file size can get pretty enormous pretty quickly. Apparently, the next release of Inkscape (0.46, arriving within the next week or two) is supposed to improve PDF/Illustrator support greatly.

Tips and Tricks
In the original spirit of this blog, here are a few things that I've found or read about during my time with Inkscape.

1) As far as I can tell, you can't actually embed images into a document permanently. This means that they're linked - and if the source images move, this can create problems. To get around this, I usually create a directory for my Inkscape file, and a subdirectory with the photos that are going into the document. This way, I can move the whole directory around, and the links are never broken.

2) If you use arrowheads in your figures, but want them in a color other than black, follow this little hint. Select the path with the arrowhead or other marker whose color you want to change, and then go to Effects > Modify Path > Color Markers to Match Stroke. That should fix it! Unfortunately, you'll have to do this each time you modify the color of the stroke.

3) I've read (but haven't actually attempted myself) that exporting Illustrator files to a standard SVG format usually works pretty well for later importation into Inkscape. As mentioned above, Illustrator support is supposed to improve tremendously in the forthcoming release of Inkscape.

4) I learned that hard way that PDF and EPS and some other formats don't play well with bitmaps that have transparency layers (often found in PNG or GIF files). This is no fault of Inkscape's - just a consequence of the file format itself! So, it can be quite handy to use a path to clip out the portions of an object that you don't want overlapping with other objects.

The Bottom Line
For most "casual" users (meaning most paleontologists I know), Inkscape will do you quite fine. The die-hard graphics guru may want to give this a try, but probably won't be making the switch quite yet. Be aware of some quirks (read: limitations) with import and export, and look forward to substantial improvements in upcoming versions. Inkscape is a program that should continue to improve (it's not even to 1.0 yet!), and will hopefully join the ranks of "classic" open source programs such as GIMP and

Polling Thanks

A big thank you to everyone who contributed to the OS poll last week. It's really helpful to know who's reading this site, so that I can work on describing the software that has the most potential to be used by the most people. As you can see on the results (which are still posted as of today), 2/3 of the respondants use Windows, and 1/3 each use Mac or Linux. I am also impressed to see two Unix users on the list also (you outgeek me!).

The good news about open source (and free) software: usually, it's available in Windows, Mac, or Linux versions. The mixed news: sometimes it works better on one OS than another.

Thursday, March 13, 2008

Choosing a Graduate School V

So here we come to the end of the series. I could probably write 50,000 more posts on the topic, but everyone probably wants to get back to reviews of computer software, right? This post contains some miscellaneous tidbits.

The GRE's (Graduate Record Examination) are daunting, stressful, and absolutely necessary to get into graduate school in the United States. The test score is only one part of the whole application process, and different schools give different weight to the GRE's. If you nail the tests, you are in good shape. If not, don't necessarily despair. Consider retaking the exam. Perhaps discuss your score with someone at the program to which you are applying, to see how big of a deal the score actually is. Work on strengthening other aspects of your application. Consider looking at "fall back" schools, if most of your "schools of interest" place emphasis on the GRE. Also, investigate if you need to take a GRE subject exam - it's not usually necessary for geology programs (because a geology GRE just doesn't exist), but some (not necessarily all) biology programs might expect a score from the biology subject exam.

Scoping Out the Program
By all means, make contact with someone (or multiple someones) in a department before applying. The SVP meetings are a tremendous opportunity to chat with students and faculty from graduate programs. This personal contact is important for two reasons - first, it gives you a chance to learn more about the program and get a feel for the personality of the people there. Second, and just as important, is that it gives the program a chance to get to know you. Graduate schools get a whole pile of applicants, and it doesn't hurt if they have a face to go with a name. A second thing to consider is a campus visit. This is also important, but perhaps less essential at the early stages. Campus visits are probably the best way to make yourself known to the faculty, and also the best way to get a genuine feel for the place. But, they can be expensive (particularly if you have to travel a long ways) and may not be the best use of your time early in the game (unless you are really, really, really serious about a particular program). After acceptances are made (or sometimes just before), some schools (but not all) invite a few students out to visit (at the school's expense). If given an invite, by all means accept (but only if you are serious about the program). Finally, if you have been accepted at a program or multiple programs, you absolutely should visit the campus before making any decisions. Never, ever accept an offer sight-unseen (even if you have to pay your own way to visit).

Should You Apply?
For any student, it doesn't hurt to ask a department if they think you should apply. Sometimes you might advised against applying to a program, by a faculty member within this program. Give this sort of advice careful consideration. Sometimes a program might not have funding or space for students - you may have to be willing to wait a year before applying. If it's strictly a matter of money, find out about fellowships or other options that might allow you to apply anyhow. Sometimes, too, a department may end up taking students in the end anyhow (even if this stinks for the students who didn't apply because they were told otherwise). If you are dead-set on a program, it probably doesn't hurt to apply regardless (unless they are absolutely insistent on a lack of money or space). Occasionally, you might be told that you are not a good match for a program or an advisor. This might hurt, but this sort of honesty can save a lot of time and heartache in the long run. Find out why you are not a good match - sometimes it's a very simple issue or miscommunication. And, be aware that different faculty in a department might have different thoughts on the students they want in the department. Some are overly pessimistic, some are eternal optimists, and some just don't care. Every situation is different.

Final Thoughts
Graduate school is an exciting time, but choosing a program can be a daunting task (whether you're at the application or acceptance stage). Weigh all factors, and don't fall in love with the first program that sends an acceptance letter. First and foremost, do what is right for you! Listen to your gut instincts, and get as much information as you can. Be cautious, but open. Be honest, and be yourself. Talk to a trusted professor, or a graduate student, or a potential advisor. You're not in this on your own, and you'll find what's right for you!

Monday, March 10, 2008

New Travel Grant

The Royal Ontario Museum has just announced a new travel grant, the M.A. Fritz Travel Grants for the Advancement of Studies in Palaeontology. M.Sc. or Ph.D. students in paleontology are eligible to apply, and the ROM is providing two awards of up to $750 Canadian each - one for invertebrate paleontology and one for vertebrate paleontology. Applications are due by Friday (March 15), so apply now! The ROM (as it's affectionately known) has some amazing collections and wonderful new galleries, and the museum is located in lovely downtown Toronto.

Friday, March 7, 2008

Choosing a Graduate School IV

The final two posts in this series will give a short look at a handful of other important factors in choosing a grad school.

Location, Location, Location
Personal preference - city versus rural, or East Coast versus Rocky Mountains - is only one part of the importance of location. As a paleontology graduate student, you will get very specific benefits from the location depending on where you live. On the East Coast, you get the benefit of having a whole ton of major museums (AMNH, USNM, ROM, etc.) within an easy flight, drive or train ride (not that there aren't major museums out west - they're just more spread out). If you anticipate doing lots of museum-based research, this can be a handy perk. But, it comes at the cost of being far, far away from most vertebrate-containing outcrops. This is where the West Coast and Rocky Mountain states certainly have an advantage! The field may only be minutes away.

Department Size
A small department can be nice for an intimate feel, but you might lose out on opportunities for collaborations or advice that you might get in a larger department with more faculty and students. If you build contacts in other departments, however, you can overcome some of this disadvantage. Of course, some large departments can have the problem of each student being a little fish in a big pond.

The Right Timing
How long does it take students to finish? For a master's program, 2 years is typical and 3 years is the acceptable maximum. If students consistently take more than 3 years to finish a M.Sc., this can be a very bad sign - either bad advising, an unmotivated student body (avoid this sort of program like the plague!), or departmental politics. For a Ph.D., 5-7 years is typical (and even 8, sometimes). A 10 year Ph.D. program might be something to avoid, too. This is not to say that life circumstances (having a child, unexpected illness, or other event) won't sometimes add a year or two to graduate school, or that one or two students take an inordinate amount of time to finish - this happens, and the most important thing to consider is how long the typical student takes.

Job Prospects
After finishing graduate school, it's really nice to get a job. Find out the track record of graduates from a program, and find out what kind of jobs they end up in. Do these jobs mesh with what you're interested in? Does anyone actually get a job in paleo? Do the students drop off the face of the planet after graduation? If you're interested in a career in academia, but all of the students get jobs as collections managers or technicians, you might want to look elsewhere (and vice versa). If you want a job at a big R1 university, but most of the students that graduate from a program end up teaching at small liberal arts colleges, you should also be wary. But, also leave the option of your career goals changing through the course of graduate study!

Up next: Tests, Campus Visits, and Final Thoughts

Wednesday, March 5, 2008

Poll: What's Your Operating System?

In an effort to learn a little more about the readers of this site, I've added a poll on your operating system preferences (at the right-hand side of this web page). Vote early and vote often (or at least vote early)!

Tuesday, March 4, 2008

R for Paleontologists

Quite by accident, while searching for the answer to another question I had about R (a powerful open source statistical language), I ran across a nice set of PDFs from a short course called, "Data Analysis in Paleontology for R." Gene Hunt, curator of Ostracoda at the Smithsonian, ran this nearly two years ago. The PDFs contain slides on topics ranging from the basics of loading data to running a PCA or correcting for phylogeny. As an added bonus, each includes some short exercises to practice your new-found skills. Click this text to follow the link, and then look under "Resources." The slides are posted as five separate PDFs.

I have now switched to R for nearly all of my statistical analysis needs, and have been immensely satisfied so far. Expect a post on this sometime in the next few weeks (hopefully).

Saturday, March 1, 2008

Choosing a Graduate School III

Geology or Biology?
Paleontologists straddle two worlds. The fossils we study come from the ground, and this geological context is important for better understanding the prehistoric environment. Yet, we also need to understand the biology of the now-dead organisms - all of those protuberances used to define species are muscle scars, or neurovascular foramina, or *something* that once had soft tissue. Unfortunately, it's also difficult to be a "jack of all trades." Paleontology graduate programs typically are housed in geology, anatomy, or biology departments, and your choice in this matter will have huge ramifications.

Why Does the Department Matter?
In the simplest sense, the type of department will dictate the types of classes you take in graduate school. Don't count on getting the opportunity to take strat-sed in a biology program. In a broader sense, it will dictate the types of resources and faculty at your disposal. A geology department is far more likely to have access to good thin-section equipment, the toys needed for rare earth element analysis, and experts in taphonomy or sedimentology. By contrast, a biology or anatomy department will probably have more to offer for dissecting facilities, soft tissue histology equipment, and experts in anatomy or functional morphology. So, department focus will generally (but not always) offer opportunities and constraints unique to the discipline. As noted below, your training will also define the types of positions for which you can apply later on.

Help! I Don't Have a Background in [Biology / Geology]!
This depends completely on the school and the individual. I originally wrote off my current anatomy department, because I was coming from a geology undergrad program. I didn't think they would ever want or consider a student who didn't have many biology courses - yet, it has mattered very little in the long-run. There's really no adequate preparation for human gross anatomy (other than to just take the course)! For me, and many others, it's been no problem to make the jump from geology to biology. I know fewer who have gone the other way, but that's probably just a sampling bias. In any event, don't write off a program if you are truly interested! Many departments are willing and able to help you fill any gaps in your knowledge, and it's best to talk to someone in the program itself to find out their expectations.

The most important thing to consider in this regard is where you see yourself in 20 years. Both geology or biology backgrounds probably offer equal opportunity for entry into the museum world, but if you're chasing after university-level jobs, give this topic careful consideration. Do you want to be in a geology department? An anatomy department? An evolutionary biology department?

I have a strong personal bias towards anatomical paleontology (just to be upfront). When choosing a graduate school, I saw much better job prospects with a background in anatomy. I could find a home in a biology, anatomy, or even possibly geology department (if they were more interested in a paleontologist than a stratigrapher). Anatomy offers the option of landing a job at a medical school (teaching gross anatomy), or teaching anat-phys at a liberal arts school, or finding a museum job. The options seemed narrower, and the job market smaller, for geology. Additionally, my research interests (understanding dinosaurian anatomy and paleobiology) were much more appropriate for a biology or anatomy department - I didn't feel that I would necessarily get the resources that I needed in the (quite excellent otherwise) geology departments to which I applied. Finally, I felt like I wasn't constrained when it came down to the final job search. I was able to apply for anatomy, geology, and museum jobs (with some success). So, there are no regrets in my mind about the course of action I followed.

Ultimately, the decision is up to you. Readers: feel free to chime in with your own thoughts!

Up next: Miscellanea Part I - Location, Size, Timing, and Job Prospects