Hi,

I recommend You very user friendly ImageJ:

ImageJ, National Institute of Mental Health, Bethesda, Maryland, USA, http://rsb.info.nih.gov/ij.

and also freeware WSxM:

WSxM, http://www.nanotec.es

I. Horcas, R. Fernández, J.M. Gómez-Rodríguez, J. Colchero, J. Gómez-Herrero, A.M. Baro, WSXM: a software for scanning probe microscopy and a tool for nanotechnology, Review of Scientific Instruments 78 (2007) 013705.

Good luck, I hope my hints were helpful.

Can you show the image? Maybe we can coding ourselves on the data you need.

We are using Avizo, 3D Analysis Software for Scientific and Industrial data, for data from our x-ray microtomograph.

http://www.vsg3d.com/avizo/overview

So far we have not done any particular research where the quantitative data of the foam would be needed, however I've been thinking how to do it for a long time.

In my opinion it is quite complicated to to extract such data out of the 3D image.

regards,

Bojan Z.

I agree, Avizo from VSG and ImageJ are pretty much standard. Avizo should have all the functionality. If you want to make some rapid proptyping, there is also a link to Matlab, which through its image processing library complements the functionality of Avizo.

Apart from ImageJ there are more OpenSource packages.

Fiji http://fiji.sc/Fiji

for instance is based on ImageJ but has a lot of additional functionality and filters, with some of them being potentially useful for what you have in mind.

Then there is the 3DMA Rock software http://www.ams.sunysb.edu/~lindquis/3dma/3dma_rock/3dma_rock.html

which is good in filtering and descriptions but focused on rock, not necessarily on foams.

Then there are some image processing libraries

http://sourceforge.net/projects/opencvlibrary/

Maybe you can also try Paraview (free software), rather nice for visualisation and dealing with 3D datasets: http://www.paraview.org/

Some of its features are depicted in: http://www.paraview.org/paraview/project/features.html

You might need though to convert your data to a different format, though quite some formats are accepted

If you're going to do imageJ, check out Fiji and its TrakEM2 project. These really look apt to what you need.

Thank you All for your swift and constructive replies.

Now we are going to test your suggestions.

Alain

ImageJ is a good solution. There is also some freeware for thresholding and percolation analysis available as part of the Visible Cement Data Set at

http://visiblecement.nist.gov

Good luck.

Sounds like you have quite a few good suggestions. My experience with micro CT was that the system on which the scans were done also contained very good anaylsis software (pore sizes, connectivities, tortuosities etc. Maybe you should go back to the scanner and check out the software on the machine.

@Deon: yes, you are right, but the system was working with Aphelion, which is not able to do what I'd like to do, at least in its standard (2D) version. Hence the purchase of the 3D extension. But without a serious support and with so complicated tool, I just lost more than 8000 €. Bad luck.

Alain

The microtomography data that we typically deal with are porous rocks, which have a very similar structure to foams. I use Avizo Fire for most of our quantitative analysis, and recommend it very highly. Avizo has modules for quantifying pore size, throat size, interconnectivity of pore network, surface area, etc. If you are familiar with programming you can write your own Avizo modules or export to Matlab for more specialized data analysis. You can even export your geometries to multiphysics softwares for finite-element analysis (FEA), though this is not a trivial task for Avizo. Other softwares, such as ScanIP, are better for image to mesh conversion for FEA.

You can get a free 1-month trial license for Avizo from their parent company VSG. I highly recommend doing this.

Alternatively, the softwares ImageJ and Paraview are free, but I find the learning curve for ImageJ to be a bit steeper. I don't know much about Paraview.

Hi,

Another option for 3D quantitative analysis is CTAn, the analysis software from Bruker microCT. You can download a demo version of this program through their website. (http://www.skyscan.be/products/downloads.htm - scroll down till you see the CTAn software). In the demo version, it is not possible to save the results, but if, after a first trial, you want to experiment a bit more, you can ask for an evaluation version of three months.

Hi Alain.

We have Avizo Fire which is ok for foams directly foamed. On other kind of foams, like replica, the algorithm which is behind the quantitave analysis does not apply. Bear this in mind

Hi Alan,

Which microCT scanner did you use for acquire those images?

Because how previously mentioned here, CTAn (Bruker, SkyScan microCT/ http://www.skyscan.be/products/downloads.htm) is an good option, or Scanco Medical AG Software (http://www.scanco.ch/en/systems-solutions/software.html) is an awesome option as well. And anyone microCT scanner has the Software available in the package! I've been worked with both. And I can help with both!

Hi there,

this website contains a collection of fantastic tools:

http://www.ctlab.geo.utexas.edu/software/

For your interest, I also attach a fresh review paper that introduces a few tips and tricks plus a good reference list.

Cheers

Christoph

Dear Alain

The GeoDict software (http://www.geodict.com) may also be of interest to you.

They will provide a trial license so you can test for yourself if it does help.

It provides both geometric analysis of 3d images and pde-based effective property computations on 3d images.

Best regards,

Andreas

Hello guys  am PhD student at Durham University . Am Using avizo 8 which helps me for identify grain size distribution in my sample, but i have no clue which module i have to use for compute connectivity. I would be grateful if you get me some feedbacks.

Hi Rikan. If you skeletonize your pore network, you can quantify connectivity -- though connectivity can mean a lot of things here. Avizo's skeletonization module allows the user to fairly easily compute quantities related to network connectivity from the network skeleton. If you don't have that Avizo skeletonization module, ImageJ (or Fiji) will compute a skeleton network from a binary pore geometry.; though getting quantitative conenctivity information from the ImageJ output may not be so easy. You can check out a workflow in this paper and online supplement.

http://www.sciencedirect.com/science/article/pii/S0012821X13007000

Dear Alain, if you're still looking for software that can perform quantitative analysis of micro-CT, you might be interested in ScanIP, the software developed through my company Simpleware (http://simpleware.com/).

You can order a free trial version here if interested: http://simpleware.com/software/trial/

How can use imageJ to analyse the percolation threshold? 

best regards

Saad 

 I do not know if you are still looking for a quantitative analysis software for foams, but in case if you still are looking for it, we have developed one recently. To see the available features, please click the link below.

We haven't yet decided if this will be distributed freely, but we are open for collaborations. 

Regards,

Kodanda

https://kodanda.wordpress.com/2015/05/28/psrecon3d-a-computer-tomographic-reconstruction-and-analysis-software-for-porous-structures/

I'd also like to add that if you, or anyone else, are looking for materials/porous characterisation software, you might find the Physics Modules for my company Simpleware useful to try. http://simpleware.com/software/physics-modules/

Best,

Philippe

Software (free) I have not seen here being mentioned:

Mango

http://ric.uthscsa.edu/mango/index.html

Drishti

https://sf.anu.edu.au/Vizlab/drishti/features.shtml

imorph (this is probably rather whay you are looking for)

http://imorph.sourceforge.net/

In case some C-coding etc. is not an issue, look for ITK/VTK or diplib

I would defintely recommend you visit www.MIPAR.us. Segmentation is paramount in a problem like this (in most actually), and this is what MIPAR specializes in.

It is very powerful and intuitive 2D/3D image analysis software written by scientists/end-users and is about to be released as a free trial on December 14th. You can sign up on the site as well as submit images/datasets to test.

There are many image analysis options available, but I think you may just find MIPAR to be something special if you give it a try!

I do not have alternate/additional proposals but also very much appreciate all the answers and suggestions, as the scanner used to analyse my samples is off site, and the free version of the software that I have to analyse/visualize the data on my own computer is very limited.  I will try the suggested packages as I also, like Alain, would like to perform detailed analysis of porous structures.  Best regards. Deon

We have just released our source Fortran code in https://github.com/Liujie-SYSU/CTSTA accompanying the publication of a paper in Computers and Geosciences.

The code is specifically designed for quantitative analyses of microtomography. ImageJ and Avizo can do some quantitative analyses, but are very limited.

Hope this information is helpful.

Article Computational challenges in the analyses of petrophysics usi...

If you do not need a GUI but are into Python then consider scikit package:

http://scikit-image.org/

Hi Misagh,

If you could post an example image, I'd be delighted to show you how to solve your problem.

Cheers,

John

Hie, 

I also have some problem in analyzing CT scan images of rock core specimen. My intention is to determine the length of crack from stack of image in 3-Dimension. Currently, I am using skeletonisation technique in ImageJ. But, I am not able to quantitatively determine the length. 

Please suggest possible solutions. 

Dear Neel,

are you able to segment the cracks?

Best,

Alexander

how we can find out the 2D porosity of each slice of the sample?

I would highly recommend our MIPAR software package. Our clients do this work all the time and we often work with them on this. Trial available at http://mipar.us/trial and expert training anytime at http://mipar.us/training. Also send our support staff an image at http://mipar.us/try-image and we'all send back a custom recipe for your pore detection!

Cheers,

John

Mr. Rack, 

I am successfully segmenting the crack features from the images. Currently, I am dealing with binary images of crack. I want to quantify the cracks in 3Dimensions using the binary stack. 

Dear Neel,

How do you determine the length of crack from stack of image in 3D and quantify the cracks in 3D? I am currently working on this but has no clue.

Thank you. 

Larry

If you have a 3-D binary image, you can run a percolation-type analysis (burning algorithm) on the 3-D data set (as a 3-D array for example) to isolate individual cracks. But, if they are all connected into basically one single crack, I am not sure if anyone has something like a watershed segmentation algorithm for cracks (usually used to separate relatively spherical touching objects such as air voids, particles, etc.). Some basic percolation-type codes are available at:

http://visiblecement.nist.gov/programs.html 

Good luck,

Dale

I recently came across CTvoxel, a small and free software by bruker-microCT, see http://bruker-microct.com/products/downloads.htm

- not many features but a simple way to get volume renderings.

Avizo is good but generally the license prices of these software are high.

Imorph is a free software devoted to the cellular material caracterization. It vas been developped for metalic foams quantification. Imorph.fr

To detect cracks after binarization you can use the shape classification algorithm of imorph that can segment tubular structures and plate like structures

Hi,

image pro plus may also be a good choice.

Hi,

Except for the ImageJ, I would recommend the VoTracer to be an alternative choice for its easy operation and friendly interface for volumetric image visualization and segmentation.

http://www2.riken.jp/brict/Ijiri/VoTracer/index.html

Hopefully, it works for your use.

Regards,

Kaige

Paraview 5.2 is good one. ImageJ is very good too.

I recommend you to use AVIZO software to get quantitative information， it is really convenient to make your intention come true. However, the licenses are expensive.

I have use the software to quantify the macropores in loess， please see our publication :Article Quantification of macropores of Malan loess and the hydrauli...

Hi,

plug'im ! is a new free access software for signal, image and volume processing. It aims to provide easy-to-use operators. In particular, some numerical descriptors for materials characterization are already available and others will be avaiblable soon.

The link for the software and the different plug-ins:

https://www.plugim.fr/plugin/list/2/plug_last_update/desc

Hi all,

I personally suggest PCAS, which was developed by my colleague in Nanjing University.

It is free and friendly to use. The algorithms were documented and published. Here is the link: http://matdem.com/content/?838.html.

Hope you find it suitable for your work.

All the best,

TCN

Can the Image J give the value of Porosity volume?

The Avizo software is a very powerful tool to analyse Micro CT images.

I recommended using ImageJ, a software developed by the National Institutes of Health of the United States of America. It could be freely downloaded at the website as follow https://imagej.nih.gov/ij/ . Good luck.

I recommanded to use the Avizo， however the price for the license is high

I used to use the amira software to deal with the gas hydrate CT images for 3D construction. I recommend it.

I have recently seen a lot of positive feedback and news about the DragonFly software: https://www.theobjects.com/dragonfly/index.html

- anyone here ever used it?

Dear Dr Alain Celzard, I answer right away, but I can. It will take time to solve your problems, graphic accelerators, etc. We are implementing new mathematics, see the latest draft articles in Russian. I do not have data from micro-tomography, radars, etc.

Yours

Evgeni Terentiev

Hi,

I haven't see 3Dslicer in the list: a good 1st implementation, and you can easily add Python script.

I didn't try to use it in a context like yours, by the way.

Jérôme

Somebody suggests Image J, which is free and easy, but it not that perfect. Avizo software is expensive and can satisfy our requirements, but you can get the authority free for one month by registration. Good luck.

I can do it on the Mathematical Microscope, but now I have no data from the micro-tomography.

I can do it on the Mathematical Microscope, but now I have no data from the micro-omography.

Dear Dr. Tunhe Zhou, I can write programs to analyze images from a micro tomography, it will take me time. Check out my more complex work on BH.

Dear Dr. Tunhe Zhou, I can write programs to analyze images from a micro tomography, it will take me time. Check out my more complex work on BH

Dear Dr. Claudia Romero Rodriguez, I can write programs for quantitative analysis of micro-tomography images, it will take me time. Check out my more advanced articles on gradient morphology and super-resolution BH images.

Hello

I suggest you the sofware Dragonfly

https://www.theobjects.com/dragonfly/index.html

there is an open version of the software which can do all what you need. The company is open to academic collaborations. The owners all come from the research environment and have a very good record

Hoping this can help, good luck

Colleagues, the Mathematical Microscope is an ideal tool for Ultra-Resolution images from various measuring instruments, see our presentation.

The Tutorial T3 on the next ESRF Users Meeting is dedicated to Volume Image Analysis incl. hands on for different software pages:

http://www.esrf.eu/UM2021/Tutorials#collapse1d93994f-0a4c-49e3-981b-8182889e98302

Yes I can, I need time to write this mathematical software. I have close examples of super-resolution images of Black Holes.

It may no longer be of interest, but I can suggest looking for alternatives in various programming language rather than proprietary software packages.

Most of what you are listing is implemented in the software Pore3D (from the Elettra Synchrotron facilities in Trieste) and available on Github: https://github.com/ElettraSciComp/Pore3D. The code is available in IDL language. For further info, you can refer to the following paper:

Article Pore3D: A software library for quantitative analysis of porous media

If you are looking for a proprietary software, the easiest way is to run Fiji on a powerful computer and download all relevant plug-ins.

Dear Dr. Alessio Veneziano , I need to find the time and write good software for quantitative analysis of images from micro-computer tomography. But, perhaps, in microtomography it will be necessary to redo the digitizing blocks to obtain more accurate images. I have some new math, see Black Hole Image Super Resolution. Programs on MatLab need to be remade for 3D data from microtomography - a lot of work - who will pay.

Perhaps Dragonfly can help you

Yes, I have a new math, I need to implement everything in a 3D case, see my 2D examples.

There are new packages like Ilastik www.ilastik.org

or IPSDK www.reactiveip.com/image-processing/

they have good implementations of the RandomForst type of classification. DragonFly also has that. Ilastik is OpenSource.