I have analyzed tons of Golgi-Cox material. Do you need something to deal with data already collected (i.e. you have already performed neuron reconstructions), or do you need something to actually perform the reconstructions and collect the data? 

The problem of too many neurons to analyze is inherent with Golgi-Cox staining.  It can be both a blessing and a curse.  The answer is to randomly select from your region of interest and have good criteria for choosing which cells to analyze (dark staining, can follow whole dendrites from soma to tip, not too much overlap with surrounding cells/dendrites/blood vessels). How many cells to analyze is study specific.

If you are looking for software to help perform, record, and analyze dendrite reconstructions, Neurolucida is at the top of the list. Easily the most user-friendly at every stage. This is clearly the expensive option though - you will need to get their equipment/software. With Golgi-Cox, you are likely going to be doing manual reconstructions - very labor intensive, but this program helps tremendously. The automatic/semi-automatic reconstructions do not seem to play nice with Golgi-Cox material from my experience. 

If this is not an option for you, you can look into either NeuronJ  (http://www.imagescience.org/meijering/software/neuronj/) or Neuomantic (http://www.reading.ac.uk/neuromantic/). These are free, but will likely be less user-friendly.  Manuals can be found online. My understanding is that NeuronJ will only handle 2-D images, but I believe Neuromantic can handle image stacks. I have limited experience with them personally, but many people use them. 

There is also a group at Janelia Farms creating an interesting program that will hopefully be available next year, and could probably be used for 3-d reconstructions from Golgi-Cox. Might be possible to get an early development trial. 

Feel free to contact me, but I hope this helps.

Hi Wei Y,

You could try Cellprofiler. It is pretty good for segmentation and quantification of images especially fluorescence images. ImageJ would also work but I personally find it a bit more challenging to work with.

I have analyzed tons of Golgi-Cox material. Do you need something to deal with data already collected (i.e. you have already performed neuron reconstructions), or do you need something to actually perform the reconstructions and collect the data? 

The problem of too many neurons to analyze is inherent with Golgi-Cox staining.  It can be both a blessing and a curse.  The answer is to randomly select from your region of interest and have good criteria for choosing which cells to analyze (dark staining, can follow whole dendrites from soma to tip, not too much overlap with surrounding cells/dendrites/blood vessels). How many cells to analyze is study specific.

If you are looking for software to help perform, record, and analyze dendrite reconstructions, Neurolucida is at the top of the list. Easily the most user-friendly at every stage. This is clearly the expensive option though - you will need to get their equipment/software. With Golgi-Cox, you are likely going to be doing manual reconstructions - very labor intensive, but this program helps tremendously. The automatic/semi-automatic reconstructions do not seem to play nice with Golgi-Cox material from my experience. 

If this is not an option for you, you can look into either NeuronJ  (http://www.imagescience.org/meijering/software/neuronj/) or Neuomantic (http://www.reading.ac.uk/neuromantic/). These are free, but will likely be less user-friendly.  Manuals can be found online. My understanding is that NeuronJ will only handle 2-D images, but I believe Neuromantic can handle image stacks. I have limited experience with them personally, but many people use them. 

There is also a group at Janelia Farms creating an interesting program that will hopefully be available next year, and could probably be used for 3-d reconstructions from Golgi-Cox. Might be possible to get an early development trial. 

Feel free to contact me, but I hope this helps.

Hi Wei Y,

You could use ImageJ. It is really user friendly. I personally am using it from last 3 years. I have done some experiments with Golgi staining and I have used ImageJ to analyse it through line scan and then it gives you a profile of your staining pattern through that line.

Hi Wei Y,

I agree with Ekta Mayur Dembla. Image J is a free and easy software to use.

Thank you all. I trying your sugestions. Thank you again.

HI Wei,

We also use Image J a lot, but also have access to neurolucida software. Comparing the two, I'd have to agree with the posts above that Image J is an inexpensive and worthwhile option. Feel free to write if you'd like any of our protocols for doing the analysis.

We used Neurolucida (http://www.mbfbioscience.com/neurolucida) to measure dendritic length, complexity, tortuosity, surface area, volume, and a whole other host of data that the program automatically outputs after you trace a neuron. Using stereology to randomly select a few neurons to analyze, you don't have to analyze all the neurons within a region or tissue section. With the right stereology parameters, you can analyze just a few (as few as 3 neurons per animal) golgi-impregnated neurons with a Microbrightfield stereology set-up. This paper out of my former lab might be of use to you. It is a 2013 J. Neurosci. methods paper that describes protocols for obtaining optimal golgi-cox staining, which will make any data analysis much easier. It sounds like you already have your tissue stained though, so this won't help you there, but definitely look at the paper for the future.

Thank you for the paper. Yes, my tissue was already stained. But learning something new will be helpful in the future.

Hello Wei:

If you have taken images with a good microscope (Nikon, Leica, Olympus etc), the company itself comes up with its' own software to analyze the images. If not then I found Image J as a substitute software for doing all those works you have mentioned. It's downloadable free and easily operable, just follow their instructions. Hope it helps.

There are many softwares as suggested above by most of the people. However I have used Motic Cam Software v.2.0. Its available upon registration. 

Hope this helps.

We used the Stereologer software (SRC Biosciences, Tampa, FL) to quantify total fiber length (40x, na 1.4 oil) and total numbers of neurons and dendritic spines (60x, n.a. 1.4 oil). It takes about two hours to collect data for each reference space of mouse brain (neocortex, molecular layers of dentate gyrus, CA regions). I'm happy to share these results, methods, etc. directly with anyone interested (email me at [email protected]). This work will also be presented at the 2018 Soc. for Neurosciences meeting in San Diego.