Check out this fantastic blog from Dr. Peter Falkingham

https://peterfalkingham.com/2019/02/18/free-software-for-ct-segmentation-2019/?fbclid=IwAR1dbSLCWJF100BAQoix5mEtnwXpJfJuTAXof3P7smdWD27LXfbQ2g_QfjU

Cheers, John

Hi, maybe Imod?

https://bio3d.colorado.edu/imod/

Dear Andreas Löscher,

I sometimes use ORS Dragonfly. It is free for academic purposes.

Best wishes,

Anneke

Dear Andreas Löscher,

Bruker has some free software for several kinds of analyses. You can download them here: https://www.bruker.com/products/microtomography/micro-ct-software/3dsuite.html

I have also used VG Studio Max, available here: https://www.volumegraphics.com/en/products/vgstudio-max.html

Best whishes.

Hi, Andreas,

I use to work with ITK-Snap with my students. It is a snake algorithm that work well... depending the things you want to work with.

Dear Andreas Löscher,

I use TIVMI (Treatment and Increased Vision for Medical Imagin), http://projets.pacea.u-bordeaux.fr/TIVMI/index.php?page=kesako

It has proven to be very precise : Guyomarc'h et al., 2012 : Three‐dimensional computer‐assisted craniometrics: A comparison of the uncertainty in measurement induced by surface reconstruction performed by two computer programs, In. Forensic Science International, 219(issues 1–3), 221–227.

Best wishes,

Dany

I assume you are looking for Image Segmentation software, rather than CT dataset reconstruction. Reconstruction has a very specific meaning for CT and micro-CT.

The two I could recommend are ones mentioned above; SPIERS and Drishti. I mostly use Drishti for data visualisation rather than segmentation, but my understanding is that Drishti loads all data on the GPU. Therefore anything without a beefy GPU is likely to have issues. Might be different for DrishtiPaint though.

SPIERS on the other hand I understand just loads the images in, much like ImageJ or Fiji. You cannot render things on the fly unless the software has substantially changed since last I saw, but it should definitely be more usable from the comfort of your own home.

Hope this helps

Paul

Hi Andreas

There are several options to create 3D surfaces from CT or micro-CT data. If you want create 3D surfaces (data visualization) and/or do segmentation you can try InVesalius, Drishti, Dragonfly and 3DSlicer. These are freeware.

all best,

Miguel

What about soft tissue segmentations? Are there any software that are more appropriate than the others to do so?

Davi Lee Bang you can try with the freeware I mentioned previously. Depending of the tissues and the species you are interested some of them can work better than others. I notice that you are from Brazil, so InVesalius is a very nice option for humans and was developed in Brazil.

with kind regards,

Miguel

I agree with Anneke, I can highly recommend Dragonfly ( https://www.theobjects.com/dragonfly/). You can apply for a free licence for non-commercial purposes.

What about free software to generate a 3D model from a series of rotating CT scan images (TIFF format)?

Thanks in advance!

You can transform the TIFF images to DICOM and use several free software like those mentioned previously.

Thanks Miguel,

Would you recommend me a free software to transform the tiff images to DICOM data?

Thanks!

Your welcome. In InVesalius you can upload TIFF images (https://www.cti.gov.br/pt-br/InVesalius) and in ImageJ you can do the transformation. Best

Thank you so much!!!

Your welcome Fabio!

Cheers

I have tried to use Invesalius, but I can't upload the images (derived from micro-CT scan) even when I did reduce the quality (%) or number of peaces excluded to each used one. I use windows 10, 64 bits. How can I solve that?

What software you recommend to generate 2D virtual slices from a series of rotating CT scan images (TIFF format)?

Do you mean reconstruction or visualization? For reconstruction there is a free software MuhRec (https://www.psi.ch/en/niag/muhrec ). For segmentation and visialization the best free software definitely will be ImageJ but it does not have any more advanced funcions for segmentation (as compared with amira/ avizo)

Now MorphoDig 1.5 imports 3D µCT dataset. Would be an interesting option.

Hi Andreas Löscher ,

You can also try Dragonfly software (www.theobjects.com) from Object Research Systems, it is free for non commercial use.

Dragonfly supports TIFF format and this video tutorial will help with importing your data : https://vimeo.com/227961790. You will be able to create a 3D reconstruction of your image stack.

Do not hesitate to contact me if you want more information.

Inserting topic

Avizo is the best software for 3d visualization and quantification /phase segmentation of materials.

Avizo or free non academic Dragonfly is best

I've had a lot of success with 3D Slicer. Much faster, more memory efficient, and more sophisticated than Image J in my experience. I had a number of scans I couldn't view volumes of in ImageJ without memory faults because I only have 16GB of RAM, but I've had no problems with the same scans in 3D Slicer.

Its available on Mac and PC and there is a great series of tutorials available on youtube:

https://download.slicer.org

https://www.youtube.com/playlist?list=PLPZ7CVzTCu91rj7XjJcSIk-6Q0G4ycUID

Dear Andreas,

I may be a little late to the party, but I feel this thread may be a useful place to collect §D-opensource software mentions, so I´ll drop my 2Cents regardless:

There is Drishti, as many have pointed out, which is a very powerful suite, especially tailored to the needs of biologists. It has a steep learning curve, but there are tons of tutorials available, and once you got the basics, it´s fantastic. I used it after Amira, and I was very happy, and I love the Renderer:

https://github.com/nci/drishti

https://www.youtube.com/user/900acl/playlists

Then here is IMOD, that includes 3dmod for segmenting and creating surface meshes:

https://bio3d.colorado.edu/imod/doc/3dmodguide.html#ViewingImage3D

The IMOD suite mainly is written to deal with tomography data, but the segmenting tools are quite powerful once you got the hang of it

Then the TrakEM suite included in the FiJi distribution of ImageJ:

https://imagej.net/plugins/trakem2/

It excels at registration and elastic alignment, and is especially suited to serial sectionings and/or stitched mosaic images.

People have also done amazing things using the trainable WEKA plugin:

https://imagej.net/plugins/tws

Another powerful tool for volumetric data that I am a little less familiar with, is Microscopy Image Browser:

https://forum.image.sc/tag/mib - Forum

https://mib.helsinki.fi/ - Project page, seems to be down atm

I know a guy doing FIB who used it, and was very happy with it.

And there is segmenting funcionality in Ilastik, too, although I haven´t used that feature of Ilastik yet:

https://www.ilastik.org/documentation/voxelsegmentation/voxelsegmentation

https://www.zmb.uzh.ch/dam/jcr:ba677a17-3410-45be-90ed-f305cc78457b/2019_ZMB_Ilastik.pdf

Two words in general:

RAM, OpenGL

Volume graphics

dragonfly is limited software as compare with volume graphics. ncolume graphics have lot of parameters to operate.

Dragonfly is actually quite good. I dont know ncolume graphics but Dragonfly has a lot of parameters to operate, I will be happy to show you

avizo

I don´t think, Amira/Avizo are Freeware. I know the programs from a couple years back, and they were notable for being extremely expensive in comparison to their performance. The large data pack extension alone was in the 4 digit range.

Our lab uses a combination of 3DSlicer and Dragonfly! 3DSlicer has a great open-source community for biomedical imaging applications, which can be leveraged for image analysis in additive manufacturing.

yOU CAN EMAIL bRUKER COMPANY FOR THEIR ctan SOFTWARE. nORMALLY THEY DO PROVIDE FREE ACCESS FOR 1 MONTH.

subscribe trail version of volume graphics or dragon fly for your 3D reconstruction of your mCT data. I think it is more enough for you because you are student only na.

Hi Andreas, I use and recommend ImageJ-Fiji software that is free and installable in PC, MAC, and Linux. It has large number of plug-ins and capabilities that I could not find in others, especially it has machine learning plug-ins, Trainable Weka, in addition yo 3D stacking viewing and even 3D image stack machine learning for segmentation, Trainable Weka 3D.