Software to Analyze Tree Rings
Many computer programs are available for developing and analyzing tree-ring data. If you have questions concerning any of the programs, contact the original author of the individual program listed. If you or anyone you know has developed computer programs that make an aspect of tree-ring research any easier, by all means, let me know so that I can consider placing it on this page. If you're not sure where to start, begin with the Dendrochronology Program Library (DPL) as this is fairly comprehensive and has excellent documentation.
DendrometeR analyzes high-resolution dendrometer data using both daily and stem-cycle approaches. The package contains customizable functions to prepare, verify, process and plot dendrometer series, as well as functions that facilitate the analysis of dendrometer data (i.e. daily statistics or extracted cyclic phases) in relation to environmental data. dendrometeR is available for download from the Comprehensive R Archive Network website (CRAN), and is provided with extensive help pages. To install dendrometeR from the R console, type 'install.packages("dendrometeR")'. All functions are customizable and designed with entry-level users of R in mind.
Tellervo is an open source desktop application for measuring and curating dendro samples. It is available for MacOSX, Windows and Linux from http://www.tellervo.org. This first release concentrates on measuring, organizing, and curating samples.
Some key features include:
- User friendly graphical interface
- Built upon the Tree Ring Data Standard (TRiDaS)
- Import/export support for 22 dendro data formats
- Support for standard measuring platforms
- Integrated 3D mapping with GPS, WMS, KML and shapefile data import
- Barcode-based curation of samples
- Relational database server for all data and metadata
- Security architecture with fine-grained permission controls
Without a doubt, this suite of programs, written by Richard L. Holmes, Edward R. Cook, and Paul J. Krusic, has had a great impact on the way the dendrochronological community analyzes tree-ring data. Routines are provided to edit tree-ring data, change formats, verify reconstructions, read or create files in spreadsheet formats, and estimate missing climate or tree-ring data. To make downloading an easier process, I provide links directly to the individual zipped files.
1. When you click on one of the links below, a window should open in your browser, asking whether you wish to run the file or save it to your hard disk. Select to save the file to your hard disk -- it helps to already have a folder on your hard disk named "DPL" where you can save these files.
2. Next, you should read the brief descriptions for the different routines in this comprehensive suite of software, and be sure to read the disclaimer by Richard Holmes at the end of the file.
3. I strongly recommend also downloading and unzipping the file "document.zip." You will then have text files that contain more comprehensive descriptions of these programs. These text files can be viewed with any word processor, such as Wordpad.
4. Now, choose one of the files in the list below, and save it to your hard disk, perhaps in the folder named "DPL."
5. Once they're downloaded to your hard disk, simply decompress them. These will create the "exe" files for each routine, for example, "cofecha.exe." To run, simply double click the file name.
For years, the tree-ring lab at Columbia University has been at the forefront of producing high-quality and comprehensive programs for use by dendrochronologists, thanks to Ed Cook and Paul Krusic, especially. To further make these useful, they offer all programs in both OSX (for MACS) and Windows (for PCs) versions. The programs are too numerous to list individually here but connect to this web site and you'll see programs that are also able to extract and retrieve gridded climate data at various resolutions. You'll also find very useful programs not normally found in other dendro programs, such as routines to seasonalize climate data, conduct principle components regression, even plot and edit tree-ring data!
Dendrobox was written by Christian Zang of the Technische Universität München in Germany and is a major leap for exploring the climate response in tree-ring data from around the world. The software uses over 2,400 tree-ring chronologies housed in the International Tree-Ring Data Bank and graphs out the chronology, the local climograph, and the "dendroclimograph" showing the monthly responses using correlations and bootstrapped confidence intervals.
TRiCYCLE is a user friendly universal dendro data converter application with support for 22 different data formats. It is able to convert both data and metadata (for instance species, site info, coordinates etc) between any combination of supported file formats. TRiCYCLE includes a detailed information system which provides detailed feedback when there are errors in the data file provided by the user, including if possible the line where the error is located. It also provides details of any assumptions that need to be made for a successful conversion. This freely available open source application is available for Windows, MacOSX and Linux. For more details see: Brewer, P., Murphy, D., and Jansma, E., 2011 TRiCYCLE: a universal conversion tool for digital tree-ring data. Tree-Ring Research 67(2):135–144.
Thanks to Paul Krusic, Ed Cook, and the Tree-Ring Laboratory at Columbia University, the standardization program ARSTAN has been ported over to run on Macintosh OS X and Windows OS computer, and it has the capability to produce high-resolution screen graphics! (In Windows XP, note that the Absoft software must be installed in its own folder on the root hard drive while ARSTAN itself will install under Program Files.) The graphics are nothing short of superb and are almost overwhelming. One can easily capture the graphic from the Windows screen and easily paste it into any Windows program, such as PowerPoint of Word. A truly remarkable achievement.
COREM: Windows Remote Control for COFECHA
Bernhard Knibbe (SCIEM) has created and is providing for free download a graphical interface for the popular quality-control computer program COFECHA. Simply fill in the settings as you would from the COFECHA Main Menu, run the program, and the output will open in a Windows text editor, such as Notepad or Wordpad. You will need teh latest version of COFECHA, however (6.06 or later, downloadable from above).
CORINA: Crossdating Program from Cornell
Corina is an open source, freely available, dendrochronology program used and developed by the Cornell Tree-Ring Laboratory. The main features of Corina include: Support for standard serial and USB measuring platforms; multiple cross dating measures including T-scores, Weiserjahre and Trend; standard dendro file format support including Tucson, Heidelberg and TSAP; and advanced graphing support. Corina is written in Java and so can be run on most operating systems include Windows, Mac OSX and Linux.
This software was developed by Dr. Franco Biondi and his colleagues at the University of Nevada, Reno Tree-Ring Laboratory. This software is the first that allows correlation and response function analyses of the climate/tree growth relationship using both evolutionary and moving intervals. Bootstrapping is performed to ensure robust estimates of confidence intervals. Input data required are monthly temperature and precipitation data as well as the tree-ring index chronology.
Written by Andy Bunn of Western Washington University, this is a new suite of programs written in R that perform similar functions to some of those in the Dendrochronology Program Library (DPL, see above). Source code is available, and scientists can download compressed files for either MAC or PC platforms. A comprehensive reference manual is also available for download as a PDF. More information on the dplR can be found in the journal Dendrochronologia 26(2): 115-124 (2008).
LignoStation is an "all in one system for surface preparation, high resolution assessment of tree-ring variables and wood density. The LignoStation follows a new concept: It produces high resolution digital scans, directly and automatically. The whole system is computer controlled. Thus you can focus on your scientific work, while the system does the routine work for you. Note: This product is developed in co-operation with the University of Freiburg, Germany and is in development."
Details: (1) Density assessment by a high
frequency probe (no x-ray source used); (2) Image
resolution: <= 20 microns (=1/50 mm); (3) Optical scans with
high-resolution camera; (4) Samples: increment cores or stem
discs; and (5) Maximum measurement length: 500 mm
Coupled with LignoStation is (1) LignoTrim: High resolution wood surface cutter; (2) LignoScan: High resolution, electromagnetic wood density scanner; (3) LignoScop: High resolution wood surface microscope-camera scanner; and (4) LignoVision.
LignoVision is software that represents a system for tree-ring scanning that works with any scanner and allows automatic tree-ring detection plus an easy manual editing function. Ring-width as well as early and latewood width can be separately stored. Besides surface scanning, it can also be used for analysis of x-ray images. The software also supports multiple image sources, such as optical scanner, CCD-camera, and x-ray scanner.
PRECON is software that statistically analyzes the relationship between climate and tree-ring variation ("PRECON": estimating climatic conditions that precondition ring widths). This software reads any tree-ring chronology in ITRDB format, then conducts a variety of statistical analyses (e.g., correlation and response function analyses) against monthly climatic factors. The program permits easy manipulation of data to test hypotheses about controlling environmental factors, climatic change, and possible growth effects attributed to environmental pollution. Harold C. Fritts (DendroPower) developed this software and is responsible for its support and distribution. Note that this software must be purchased to satisfy a distribution license agreement with a third party vendor.
"WinDENDRO is a semiautomatic image analysis system specifically designed for tree-ring measurement." This software and hardware package has seen increased use over the years, and has certain features that make it particularly appealing and well-worth considering for your research. The system works with a scanner rather than a video camera, and is tightly integrated with density analyses and stem analyses routines. The user has extensive control over the paths over which the software records measurements, and can even "train" the software to determine where the ring boundaries exist. This software also comes ready to operate across numerous Windows and Mac platforms. For technical questions, contact their Technical Support. For sales questions, contact their Sales Office.
FHX2 and its Windows version FHAES analyzes event chronologies such as those related to fire scars and other fire history studies as developed from tree-ring data. The software provides means for (1) entering and storing fire history data, (2) graphing and plotting these data, (3) statistically analyzing the fire history, and (4) analyzing the relationship between fire and climate. Statistical analyses include fire interval tests, seasonality summaries, and tests that detect changes in temporal or spatial aspects of fire regimes. The software is primarily known for its strong graphics capabilities. Henri D. Grissino-Mayer developed the original FHX2 software and is responsible for its support and distribution, while FHAES is a major collaborative effort of many different agencies to update the capabilities of FHX2.
TREERING 3.0 is a process model of the response of cambial activity and ring structure to daily climatic variations. The model provides calculations of water balance, photosynthesis, carbon storage, crown growth, and cambial activity, then provides graphical outputs showing the daily values of growth regulating processes (e.g., number of cells dividing, enlarging, and maturing) along with the resulting ring structure. The model was developed by Harold C. Fritts of the LTRR and Alexander Shashkin of the Institute of Forestry in Krasnoyarsk, Russia. Note that this is a model only.
TSAP-Win - Time Series Analysis
TSAP was designed as a platform
for measurement, database handling, analyzing, and
presentation and crossdating of tree-ring time series.
Developed for WIN by Frank Rinn and coworkers, the
architecture of TSAP is based on object orientated handling
of time series, independent from origin and format. TSAP
also supports the Tucson tree ring data format and most
TSAP has amazing graphics capabilities as well as numerous options for crossdating and standardization. A truly impressive suite of programs that works in conjunction with the LINTAB measuring system as well as with other systems. TSAP is distributed by RINNTECH - Frank Rinn, Hardtstrasse 20-22, D-69124 Heidelberg, Germany. Tel: +49-6221-70405-0, Fax: +49-6221-71405-234 email@example.com. RINNTECH now has a US-office which can be reached at firstname.lastname@example.org.
PAST - Personal Analysis System for Tree-Ring Research
PAST is a software package designed for crossdating tree-ring measurements, developed by Bernhard Knibbe Software Development in cooperation with Dr. Otto Cichocki of the Interdisziplinäre Forschungseinrichtung Archäologie (IDEA, Interdisciplinary Research Group for Archaeology, IDEA) at the University of Vienna. This software promises revolutionary visualization and correlation techniques, a new statistics engine that makes correlation runs faster than ever, sophisticated print-out routines to help publish data, improved bar graphs and graphics, and a new plug-in interface that makes it possible to customize the program with additional functionality. The software runs on a Windows platform for PCs, and a 32-bit version has been released recently for Windows 95/98 and Windows NT. From this site, one can download a trial version of the software. It is also possible to read the entire PAST32 manual online to give an overview of the program's features. PAST also supports the Tucson tree-ring data formats!
MeasureJ2X is a software program for measuring tree rings from a variety of measuring stages. The program runs on both PC and Mac hardware, supports the Metronics, Boeckler, AccuRite, and Measucron measuring systems, and standard or USB serial ports. It has full features for creating measurements of new series or editing existing series. It is designed to be used in conjunction with the COFECHA output, allowing measurements to be inserted and deleted, and for series to be shifted forward or backwards in time. The program reads and writes series in the "decadal" format, allowing its output to be used with the analysis programs available from the DPL. The program replaces the former Medir (DOS) and PJK6v2 (Mac) measuring programs and has similar functionality to those programs. The program was developed with support from the dendrochronological community and continues to be maintained through the ProjectJ2X subscription process.
These two suites of software were created by Lars-Åke Larsson of Cybis Elektronik & Data AB in Saltsjöbaden, Sweden. CooRecorder is a free standing program for registration of coordinates from scanned pictures that are shown on your computer screen. One can use CooRecorder to measure tree-ring widths by registering ring boundary coordinates, but the program is not limited to this usage. CDendro is a program for ring-width correlation analysis, i.e. dating and for building reference curves of ring-width data. This site also has impressive tutorials about normalization of tree-ring data, dating tree-ring series using correlation analysis, and the creation of reference chronologies.
THAT'S RIGHT! All kinds of free software available that provide access or display capabilities for all kinds of paleoclimatic datasets. For example, the SiteSeer software allows the user to browse the contents of the pollen database, displaying summary information and summary pollen diagrams. Singular spectrum analysis is currently big in dendrochronology, and software that conducts this very specialized process can be freely obtained! Check this out! There's even a European mirror site to cut ftp download time and your online expenses!
OpenRWL: a wonderful Microsoft Excel add-in (written by Luc Cournoyer) that quickly reads in a measurement file in Decadal format and places all measurement series in columns.
Medir: an excellent DOS-based measuring program written by Paul Krusic with some modifications by the late Richard L. Holmes. Captures and saves files automatically in Decadal (also called "Tucson") format.
Convert5: utility program (written by Henri D. Grissino-Mayer) used for converting measurement files in TRIMS, Decadal, and Catras formats into one file in Decadal or Compact formats.
CoRing: utility program (written by Oriol Bosch) capable of editing, screen plotting and converting Catras and Trims measurement files into Tucson decadal files (and Catras into Trims format).
Verify5 for DOS: utility program (written by Henri D. Grissino-Mayer) used for independently checking the accuracy of initial measurements made by technicians.
Verify for Windows: an improved Windows version (written by David M. Lawrence) of the popular Verify5 program.