| Software
and Hardware used in Dendrochronology
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.
The
Dendrochronology Program Library
Without
a doubt, this suite of programs, written by Richard L. Holmes and
Edward R. Cook, 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.
DIRECTIONS
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,
even 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 type the name of the file or run
it from Windows.
ARSTAN
for Windows
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).
LignoStation and LignoVision
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.
DendroClim
2002
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.
Precon
5.1
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
"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:
Fire History software
FHX2
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 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.
TREERING
3.0
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
- Time Series Analysis
TSAP
was designed as a platform for measurement, database handling, analyzing,
and presentation of tree-ring time series. Written by Frank Rinn of
Heidelberg and Siegward Jaekel in Leimen, Germany, the architecture of
TSAP is based on object orientated handling of time series, independent
from origin and format. 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. TSAP is distributed by Frank
Rinn, Engineering and Distribution, Bierhelder Weg 20, D-69126
Heidelberg, Germany. Tel: +49-6221-314 387, Fax: +49-6221-315 406, info@rinntech.com.
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
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.
CooRecorder
and CDendro
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.
Free
Paleoclimatic Software
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!
Other
popular programs:
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 Richard L. Holmes)
that 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. |
