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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

Current temperature conditions at the Marine Science Center

Updated December 2013: The seawater temperature monitoring is no longer functional since I moved away and someone turned off the computer. The data I collected for 2010, 2011, and part of 2012 are available as one csv file: 2010-2012_MSC_temps.csv  The time stamps are all in Eastern Standard Time (UTC-5, no daylight savings time) and the water and air temperatures are in degrees Celsius.

I put together a temporary monitoring system for the seawater temperature and air temperature here at Northeastern University’s Marine Science Center in Nahant, Massachusetts.

The monitoring system is was running using some homebrewed Labview code … Continue Reading

Printing to pdf with MS Office 2007

For those not aware, if you have Office 2007, Microsoft makes available a free download to enable you to save files as .pdf. SaveAsPDFandXPS.exe is available on the Microsoft site. It is not necessary to buy a copy of Adobe Acrobat, or go searching for any of the many free pdf printing utilities out there, just to output your Word document as a pdf file.

Pictures from Quoddy Head, Maine

Photo gallery from the Three Seas program trip to Lubec Maine. October 2010.

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