Hi James,

If you already have the image stack, then many freewares should be able to process image stack into STL relatively easily. 

If you only have TIFF, one software that I tried was FIJI. 

You can open the TIFF images in the correct sequence in FIJI. Then process them into an image stack, make the image stack binary and you can then view then using their 3D viewer plugin. 

Once you are satisfied with the 3D view you can choose to export the surface as STL. 

Hope that helps!

Thanks Kai,

I'm able to open my image stacks and 'Display as Volume' in the FIJI 3D viewer. However, I am unable to 'Display as Surface' (as needed to export to .STL). The program just hangs (I waited for 20 minutes) with no response. It could be my computer, but I'm not sure?

Yes this step tends to guzzle up most of the processing power... I could think of two suggestions. One is that you import stacks of lesser images, and you can stack the exported STLs on top of one another quite easily in many 3D modelling softwares.

Another way is to reduce the pixels in your image stack. You can do this in FIJI by Process > Binary > Dilate. I would imagine dropping the resolution of TIFF image might help too.

TIFF image stacks (esp those filled with tiny features) tend to easily go into STL file size that is not manageable by most 3D printing softwares. Any file above 40MB can cause quite a headache when you slice the file for printing so you might want to keep this in mind too.

I am quite interested in your work. Is there any chance that you could share a picture of the final product with me? :)

James,

Mimics from Materialise can import image stacks (use manual import), has powerful segmentation and editing tools, and will export STLs, but it is expensive.  You can get a trial version to see if it will work for your needs.

ImageJ can import stacks (http://rsbweb.nih.gov/ij/docs/guide/146-8.html) and export .obj files which can converted to STL with MeshLab.

Good luck with your project!

Thanks Kai and Crispin,

It turns out that my image stacks were >100 MB each! I was able to resize them in FIJI (reducing them to about 20 MB), apply 3D filters, convert to binary, open as a surface in the 3D Veiwer, and save as an STL file.

Yes Kai, I'll be happy to share a photo of the finished product with you soon.

Thanks again guys!

I am glad it works for you. Have fun printing!

Check out http://svn.softwarepublico.gov.br/trac/invesalius, a free sw for processing medical images, from Brazil...

Thanks Marcelo, I'll check it out!

Another system to check out, but not free, is Vizua... described here www.3dsystems.com/solutions/services/bespoke-modeling/tour. It's web-based, pretty neat.

Hello Everyone,

Thanks for all of your input last year. I ended up using FIJI to convert my stacks to .stl (after reducing pixels in each image stack). Our work was recently published (attached). Also, here is a photo of a 3D printed muscle cell (500x larger than actual size). Pink = cell body, Blue = nuclei. Thanks again!

Cheers,

James

Article Three-Dimensional Printing of Human Skeletal Muscle Cells: A...

Our Checkpoint software can convert an image stack to a 3D volume and extract STL surfaces from them.

https://www.stratovan.com/products/checkpoint?utm_source=rg&utm_medium=ans&utm_campaign=stack1

For me FIJI works best for binarization and scaling.

Afterwards chimera can be used (https://www.cgl.ucsf.edu/chimera/download.html) very nicely to get .stl files. Chimera is a free 3D-visualisation GUI mainly used for proteinstructure analysis and structure visualization, but it can handle 3D data of all sorts.

It is importent that the tiff-stacks has to be scaled in fiji to get isotropic voxel sizes needed for Chimera.

Sofar I did not have much of an issue with bigger stacks of around 100-200MB. Takes a while till the programm is finished, but in the end it allways did without crashing.