I am growing fungal cultures in plates and I am monitoring daily growth for 8 days. I measure the diameter in an x and y axis and use the average to estimate mean growth of the fungus. I have started using Assess on digital pictures of the cultures to look at the contrast between the background (media on the plate) and the fungus to try to quantify, in a more automated manner, the growth (area of the plate occupied by the fungus). I just want to know what else is out there that is user friendly and highly affordable (free would be ideal).
ImageJ is a very versatile and could be used for this. Therkorn and Mainelis describe a method: http://www.tandfonline.com/doi/abs/10.1080/02786826.2013.842954
Alternatively have a look at Cell Profiler's Yeast Colony Classification pipeline: http://www.cellprofiler.org/examples.shtml#YeastColonies
Or Open CFU: http://opencfu.sourceforge.net/
All are Free and Open Source. You'll have to try them and decide how user friendly they are.
http://imagej.nih.gov/ij/index.html
http://www.tandfonline.com/doi/abs/10.1080/02786826.2013.842954
http://www.cellprofiler.org/examples.shtml#YeastColonies
http://opencfu.sourceforge.net/
Please refer to article with title of "Detection and Quantification of Bacteria and Fungi Using Solid-Phase Cytometry"
Thanks, but I'm looking for something that would work with digital images.
ImageJ is a very versatile and could be used for this. Therkorn and Mainelis describe a method: http://www.tandfonline.com/doi/abs/10.1080/02786826.2013.842954
Alternatively have a look at Cell Profiler's Yeast Colony Classification pipeline: http://www.cellprofiler.org/examples.shtml#YeastColonies
Or Open CFU: http://opencfu.sourceforge.net/
All are Free and Open Source. You'll have to try them and decide how user friendly they are.
http://imagej.nih.gov/ij/index.html
http://www.tandfonline.com/doi/abs/10.1080/02786826.2013.842954
http://www.cellprofiler.org/examples.shtml#YeastColonies
http://opencfu.sourceforge.net/
OpenCFU is an open/source software that is very good to count cell colonies and other circular objects.
OpenCFU is an open-source program distributed under the conditions of the GNU General Public Licence version 3. It is available on Sourceforge (http://opencfu.sourceforge.net). A user manual and video tutorial are also provided. hope that this info is helpful.
Thanks, Miguel! I'll look into it. I used ImageJ previously, but it wouldn't outline the growth of the mycelium in culture, so I used it to obtain the diameter measurements of the culture. However, since sometimes the shape of the mycelium may be irregular, I would have preferred something more accurate like the area, but without spending too much time tracing. I also used ImageJ to count spores, and that was a bit more helpful, but it sometimes did not identify all the spores, particularly when the contrast of the background and spores in the image wasn't as sharp or when the spore density was high.
- Badges
- Science method