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ncdf4 R package binaries for Windows

David Pierce has made available a pre-packaged Windows binary version of his ncdf4 package for R. Go to his ncdf page to download the zip file you need. The current file at the time of this writing is ncdf_1.8.1.zip.


After downloading the zip file to your Windows computer, you can install this R package most quickly by opening a Rgui.exe window, then going to the menus and choosing Packages>Install package(s) from local zip files…, select the zip file you downloaded, and hit Open to have R install the package.

To use the package in R, you must run a 32-bit … Continue Reading

Digitizing data from old figures with ImageJ

Following on this earlier post concerning the retrieval of data from figures in published papers with R, here is a method for doing the same with ImageJ. This is a freely available program that should run on Windows/Mac/Linux, just like R. To extract data points from a figure, you’ll need the Figure_Calibration plugin developed by Frederic V. Hessman, available here. Download the Figure_Calibration.class file from that page and save it to your ImageJ/plugins/ directory. Then load up ImageJ.

[caption id=”attachment_1051″ align=”aligncenter” width=”400″ caption=”The example figure that we wish to retrieve data from. We can use … Continue Reading

ImageJ paint brush tool keyboard shortcut

ImageJ is easy to modify if you know a bit of Java. I don’t know any Java. But here’s what I did to add keyboard shortcuts for the paint brush tool and the line selection tool. The code is based off this help file from the ImageJ website: http://rsbweb.nih.gov/ij/docs/guide/userguide-32.html

The first step was to figure out to refer to the line tool and paint brush tools. I did this by going to Plugins>Macros>Record and clicking on the line tool and the paint brush tool in succession. The numeric codes for those tools were revealed in the macro recording window … Continue Reading

Measuring leaf or algae blade area in a digital photo with ImageJ

The following is a tutorial on using the freely available ImageJ program from the National Institutes of Health for estimating the area of a leaf or algae blade (or anything else). The process is straightforward once you understand the various steps.

You must begin with a photograph of your object, flattened and dried off as much as practical. Include a clearly visible ruler or other measuring device in the picture. Ideally you will photograph your dark leaf or blade on a light background to maximize the contrast between the object and the background.

[caption id=”attachment_1009″ align=”aligncenter” width=”300″ caption=”The original picture, … Continue Reading

BBQ controller, version 2


The smoker and temperature controller.

A few years back I put together an electronic BBQ temperature controller that regulated the air temperature in my smoker and displayed the air + meat temperatures on a computer in my kitchen, while also posting the temperatures to Twitter. More recently I have decided that setting up my old desktop computer on my kitchen counter is a poor use of space, so I set about making a more compact temperature monitor.

This time around the contraption is based on an Arduino board. … Continue Reading

Nahant coyote

I ran across one of Nahant’s resident coyotes hanging out in the church parking lot on Sunday morning. Surprisingly, it was not eating a local Nahant child at the time, despite the stated fears of a subset of our community.

June 25, 2011

Archived water and air temperatures for Nahant, MA

I’ve added the archived temperature data for the Marine Science Center to my current conditions page: http://www.lukemiller.org/seawater/. The complete timeseries, with some large breaks when the monitoring computer was shut down, can be downloaded in this csv file: 2010-2012_MSC_temps.csv (5MB, right-click and save-as). There are three columns, with the timestamps in Eastern Standard Time (UTC-5, no daylight savings adjustment), water temperature and air temperature in degrees Celsius. Missing data are recorded as NA.

Temperatures for July 2010 through May 2012 Temperatures for July 2010 through … Continue Reading

Deploying barnacle settlement plates

As the northeast slowly starts to shrug off the shackles of winter, the barnacles decide to start spawning their planktonic larvae that float around for a few days, looking for a place to settle. We use barnacles in experiments all the time, so we set out little granite tiles in the field in central Maine to give the barnacle cyprids (larvae) a place to settle and metamorphose. We can then return in a few weeks and bring the tiles back to the laboratory, where the barnacles continue to grow until we use them in an experiment. Unfortunately, doing all … Continue Reading

Time lapse of fall 2010

The video above is a series of photos, taken around 8am daily between Oct 10, 2010 and Jan 1, 2011. The view is of the backyard of my current abode. Taken with a Canon 5D (try the HD version on youtube), 35/1.4, Av mode at f/8, ISO 200. My ocean view, such as it is, reappeared around Thanksgiving, and the first snow hits December 21st.

Additionally, below is a 1-day time lapse of the snow storm that hit Boston on January 12, 2011. The images were … Continue Reading

Book Review: Practical Computing For Biologists

Practical Computing for Biologists
Steven H. D. Haddock and Casey W. Dunn
Sinauer, 2010

Practical Computing for Biologists is an ambitious book that primarily aims to demystify many of the problems that most biologists will hit at some point in their research that can be solved with a bit of simple programming. The book does an admirable job of achieving this goal by exposing the reader to a number of freely available programs and techniques for dealing with text files and other data types. Much of the book (Parts 1-4) … Continue Reading

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