Saturday, February 6, 2010

Tools and Tricks: Image analysis software for the geosciences

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Trying to find an easy way to do modal analysis on fotomicrographs of thin-sections I found two very useful and free programms to assist in such efforts. These programms are JMicroVision and ImageJ. Both of them are Java based and should function on any ordinary computer. I've been testing both of these in the last weeks and they have their uses. JMicroVision has been developed by Nicolas Roduit of the University of Geneva with image analysis of petrographic thin-section in mind and allows to do various tasks easily, like point-counting, area counting, grain-size measuring or pore classificaton to just name a few. ImageJ originated in the field of biology and medicine, was developed by Wayne Rasband from the National Institute of Mental Health, Maryland, and thus lacks a little the easy to find path as the other programm though offers a lot of tools and plugins that make-up for that short coming. What I found to be an enormously interesting feature is the possibility to make 3D images from serial fotographs or other well aligned image sources which sounds like a great tool to make 3D images from serial thin-sections of fossils. The biggest short-coming of both programmes I discovered to be the image analysis of contrast poor limestones which I am working. Neither programm manages to adequately seperate components and cements. So I have to stick to old-fashioned point-counting. Utilising contrast and color-richer sandstones or crystaline rocks easily gives great results though!

Being relatively new to the computer aided image analysis I recommend to check-out the respective websites yourself. I am sure to some of you these will be a value!

9 comments :

Miquel R (Sulema) said...

hello:
I have discovered your blog and at last You can answered to some questions I had, specially the oncoids or pisoids. I wonder if I could send You some images of some of them. Next week I go to a quarry here in valencia (Spain) with thousands of them.

Miquel R (Sulema) said...

hello:
At last I have discovered a blog where to answer some questions I had. I have been searching in a quarry here in Valencia (Spain) and I have discovered some oncoids. Could I send some images to You?
My name is Miguel

Lost Geologist said...

Miguel,
thanks for putting so much trust in me still limited but growing knowledge about carbonates. I would have liked to reply to you by mail - maybe you can still forward that.

Are you a student or a graduate of the university of Valencia? I don't want to interfere with your course work but if that is not the case, yes, please show me some cool images and I will see what I - or fellow bloggers - think about it.

Don't forget a quick description of their stratigraphy and outcrop. Can you already tell us more about the quarry?

Lost Geologist said...

An idea I just had:

Do you have a flickr or picasa account? You could upload a large number of images there and don't have to email them around. It would be much easier to share them with a large number of people.

Miquel R (Sulema) said...

Hello:
I'm archeologist, but I'm specialist in roman and medieval buildings and quarries now in Valencia Politecnic university.. My thesis is finished 3 weeks ago, but I discovered some bizarre fossils that thanks to You could be oncolites. If I'm not wrong is a 8-5 m.a quarry stone quarry but only on surface,could be older in the deep part where oncolite are. Next week I'll go to the more pictures, only I have some here. In other way I'll write to my thesis director to ampliate some pages.
I'll try to send You as fast as possible one picture that makes me think is not an oncolite but a sponge.I'll try to discover the picassa and lick to put pictures. Thank You very much
Miquel

Miquel R (Sulema) said...

sorry I can't instal picasa or flickr in my mac

Miquel R (Sulema) said...

Where I could send meanwhile 1 image of a possible oncolite or sponge?

Lost Geologist said...

Send the foto (with scale please) to my email adress. It can be found on the right navigation bar in the "About" box. Please also mail me the location of the quarry maybe I can find out more of its geology.

Miquel R (Sulema) said...

thank You, But I don't find the mail, can You send me written separatedly?
Well, the quarry is located in Godella (on google earth it's easy to find it. Is 6 km from valencia and 90% stone was taken from there.

I have 3 pictures now to send You of stones I colleced yesterday. Next week will the the great day, beacuse all levels are really beatiful with a lot of oolites and oncolites with different colors (white and black) perfectly deposited.