category archives: science

CR1 script to log balance measurements with a campbell scientific data logger

[posted: ]  [0 comments]

here’s a script to record time-series of balance measurements (weight data) using a Campbell Scientific CR1000 datalogger and a balance with an RS232 serial interface.
we have been using two dedicated scripts which vary slightly to work with two different balance models, the Mettler-Toledo MS8001TS (polled mode; should work with all current Mettler-Toledo balances based on MT-SICS) and the Kern DE35K0.5D1 (set to continuous output).

download: (.cr1 files, saved as .txt)
CR1000 script to log output from a Mettler-Toledo MS8001TS balance
CR1000 script to log output from a Kern DE35K0.5D balance1
CR1000 script to log output from four Kern DE35K0.5D balance1

if you just want to have a look at the code, the CR1 scripts are included in text form at the end of this post.

1note that, as it turns out, the strain gauge loadcell measuring system of the Kern DE35K0.5D balance makes it unsuitable for longer term measurements. to get an idea of the drift effect resulting from a continuous load on these balances, here’s a figure from a test run with constant weights: [more...]

[categories: computers & technology, science] [tags: , , ]

ICT PSY1 stem psychrometer: how to apply sensor calibration after recording a dataset

[posted: ]  [1 comment]

for the past 2+ years i’ve been working with the PSY1 Stem Psychrometer by ICT International. as with any precision instrument, calibration is a crucial step to ensure good data. however, we’ve found that with some older firmware versions, the PSY1 sometimes just dropped its calibration files and reverted to the generic factory-calibration, which reads at +/- 0.5 MPa absolute precision.
after some discussion with ICT, i’ve put together a little R script that allows the application of calibration parameters to an existing file which was recorded with any (or no) calibration. this way, you can recalculate proper water potential readings from already recorded PSY1 csv-files.

ICT PSY1 stem psychrometer: how to apply sensor calibration after recording a dataset

the complete script, documentation and more are available here: psy-posthoc-calib — bitbucket

[category: science] [tags: , ]

time lapse: microCT scanning at the australian synchrotron

[posted: ]  [0 comments]

the brodribb and choat lab groups (read: my colleagues and i) are currently at the australian synchrotron in melbourne for an experiment to study what’s going on in the stems and roots of living trees during drought. using x-ray microCT, we can look inside the wood and examine whether vessels are functional (i.e. water-filled) or blocked, without cutting into the tree (which can create a range of problems for measurement).
here’s a time lapse video showing how our eucalyptus trees are mounted onto a high-tech robot arm (0.0001 mm precision movements!), centered, and then rotated during the x-ray scan:

the resulting microCT scans have a resolution of 10 micrometers per pixel and can be reconstructed to 3D models. more about that in a future post…

[categories: science, time lapse] [tags: , , ]

non-invasive imaging of the plant water transport system using x-ray microCT

[posted: ]  [0 comments]

it’s been rather quiet in the blog lately, so i thought i’d share a peek into what we’ve been up to at work:

Hydraulic vulnerability analysis using X-ray microCT
MicroCT cross section of a Eucalyptus stem. One of the major points of critique for hydraulic measurements of xylem vulnerability and embolism is that they are destructive measurements. In contrast, non-invasive imaging has made it possible to observe xylem function and the spread of embolism in living, intact plants without destructive sampling and associated artefacts.

In collaboration with Iain Young and Richard Flavel at the University of New England, Armidale, we recently scanned the stems of young Eucalyptus trees at high resolution using X-ray Micro Computed Tomography (microCT) to visualize the loss of hydraulic function at increasing levels of drought. [more...]

how to print a timestamp with periodic output from WinWedge

[posted: ]  [0 comments]

how to print a timestamp with periodic output from WinWedge WinWedge is a simple tool to obtain periodic readouts through a serial RS-232 or COM interface (e.g. from an analytical balance). unfortunately, though, obtaining a timestamp for every data point is not as intuitive as it could be.
here’s how you can automatically add a timestamp to your periodic output with WinWedge (tested with WinWedge32 Std. V3.0).

let’s assume that you’ve already configured the basic communication (“Port” – “Settings”) and timer settings (“Define” – “Serial Output Strings” > “Interval (ms)” and “Timer Controlled Output String”). [more...]

[categories: computers & technology, science] [tags: , ]

algal collection in living pictures [lytro]

[posted: ]  [0 comments]

algal collection in living pictures [lytro] the algal collection of the department of botany (university of innsbruck, austria) is an extremely photogenic subject. i published some pictures of the collection a few years ago, one of which has since been awarded “science image” by our university’s biannual magazine.

now, i’m happy to present the first interactive “living pictures” of the collection, taken with a lytro lightfield camera.

(lytro living picture: click to refocus, click&drag for perspective shift)
(view on

somehow, it’s fascinating that you can tell these (mostly) single-celled organisms apart by the macroscopic shape of their cell colonies.

more pictures are waiting for you in my new lytro album: algal collection

mars simulation tweetup at the dachstein ice cave, austria [photos]

[posted: ]  [0 comments]

here are some pictures from the first austrian #marstweetup – a twitter event that gave 16 space-enthusiastic twitter users from all over europe a deeper insight in to the ongoings of a live mars simulation. the event took place inside the world’s largest accessible ice cave in dachstein, austria.


[categories: computers & technology, photo, science] [tags: , ]