I am trying to get a crude measure of trabeculae parameters (e.g. thickness, separation, number, pattern factor) from stained 2D sections (no micro-CT unfortunately). I'm currently using CTan (SkyScan) and will try BoneJ, but was wondering if there is other good (preferably open source) software out there.
boneJ is pretty decent for open source. GE makes a free microCT viewer/analysis package (MicroView?) but maybe only able to deal with 3D image stacks. I don't know.
Dear Mr. Bond
You can use Qwin for the measurements. The ope source software with limited functions is Scion Image or Image J.
BoneJ & other ImageJ/FijI plugins will work fine for those measurements. I used CTan for micro-CT measurements, but would prefer ImageJ for histological sections.
Look into different segmentation methods & make sure to calibrate the pictures (Analyze > Set Scale) before measuring the thickness - to get accurate readings.
It is also possible to load in multiple images (File > Import > Image Sequence) and you can run the plugins without loading each section individually- will save you a lot of time.
It's expensive, but the best I've ever used is BioQuant (http://www.bioquant.com/). Nathanial has a bone histo-specific module that does everything imaginable.
If you are looking for free and open source then Bone J is good enough. I have worked with Bone J and Osteomeasure. Osteomeasure is expensive and I am sure their are better software then Osteomeasure, not really user friendly.
Stephen, We use Image-Pro Plus for our bone image analysis. It is a bit costly, but works well for our needs. I have also heard good reviews for BioQuant, but have never tried it. Best of luck. Sean
we have done comparison between mandibular bone i Mb Crohn pat and healthy pat by using regular Btw (bitewing) ex ray radiography. You can use Jaw-X software (Crebone AB, Sundbyberg, Sweden). It was used first by Grethe Jonasson. This digital imaging algorithms to create a binary filtered image to analyse the trabecular structure in a selected area with standardized trapezoid marker. You measure the trebcular space. A cheap metod
Hi, I've written my own software, using ImageJ as an image abnalysis library. So under the hood it is ImageJ, but it has a completely stripped down user interfave, an easier to use Image display window, easier drawing tools for changing selections,and a wizard-like approach to talk the end user through the procedure. results are saved as standard .csv files, compatible with Excel. The software runs best on 64-bit systems, but for images that are not too big, good old 32-bit windows is fine. The machine should have java installed (as almost all computers do nowadays). If you're interested, drop me an email or have a look at my web page that has a few screenshots http://www.rheum.med.ed.ac.uk/biography/rvh.php. I've got a demo movie in my dropbox at https://dl.dropbox.com/u/50702312/Trap%20demo1%20HD.wmv for the program that analysis Trap stained osteoclasts on bone. I have two more programs: one that will analyse calcein double labels and one for von Kossa/van giessen stained sections for basic bone parameters and osteoid surfaces.volume/thickness. I haven't done the movies for those yet though.
Final software and source code are available from me for free. I' preparing a paper for it, but it will still take me a bit of time to finish that (too much to do, too little time).
If you're interested. just send me an email.
The terms you used are for micro CT analysis, for 2D section I use image Proplus but can not analyze parameter you want
In response to Prisana, apart from the pattern factor, where I'm not certain and would have to look it up, the parameters that Stephen wants to measure can be quite easily derived from tissue area, bone area and bone surface. Just have a look at the classic paper on standards for bone histomorphometry by Parfitt et al (JBMR 2:595-610; 1987).
Thanks to everyone for your insights and suggestions, and especially to Rob van't Hof for allowing me to use his custom analysis software.
Than you Rob, would you mind if I would like to try your soft ware, I have some work to do histomorphometry.
Hi Prisana,
just send me an email to explain what you want to do exactly, and maybe one of the images you want to annalyse. I can then check if my software works with your stains or wether it needs some small adaptation.
If there is someone that could help you with Matlab, its image analysis part is really topnotch in this regard!
Hello Rob Van 't Hof ,
May I use your custom made analysis software? I have the same issue as Stephen B.
Hi Ernest.
Drop me an email at [email protected] and I'll send you a download link and a link to the webpage describing the software. Software ids described in a paper in Bone from 2017. You can find it on my researchgate pages.