Try Cell Profiler (http://cellprofiler.org)

Thanks for the response.

We are currently using cell profiler and finding the output a little unwieldy, we are looking for something that would do a little more analysis of the data that is generated.

See Nature Methods: July 2012, Volume 9 No 7 pp627-763

This has some reviews of imaging softwares.

Hi,

you can try Image J software.

http://en.wikipedia.org/wiki/Image_J

Developed by the NIH and open source.

you can implement macros to analyse all your images the same way.

we are currently using this software to analyse and measure specific IHC staining.

alexis

Did you try CellProfiler Analyst? I believe with some tweaking it can do a lot with your data

Hello,

someone already mentioned ImageJ, but I would also suggest you to take a look on Fiji. They have been developing several plugins, some of them very specific for cellular analysis. It's VERY similar to ImageJ, but I found it more "complete", easier to keep it up to date (in terms of new plugins, etc).

For more details about Fiji: http://www.nature.com/nmeth/journal/v9/n7/full/nmeth.2019.html%3FWT.ec_id%3DNMETH-201207

Also, check this paper, they cite several softwares for biological imaging analysis: Keerthana Prasad and Gopalakrishna K. Prabhu, Journal of Medical Systems, August 2012, Volume 36, Issue 4, pp 2621-2631

Thanks for the responses.

I have tried to use Cell Profiler Analyst, but for some reason cannot get it to run on any of our computer.

We have also looked into ImageJ but found it to be a bit more technical that we would like, at this point we are prepared to actually buy some sort of package in order to save time working out all the programming etc in something like ImageJ.

Hello,

If funding is not a problem for you, and you don't like programming like what you need on Cell Profiler Analyst, you may think of InCell Analyzer software by GE healthcare. The software gave advantage of automating self scoring with final report being produced once you set up the parameters. As they are designed for high throughput screening, its is mainly designed for 96 well format. The down side is it did not give me the option to name my each sample from the beginning thus making me have to refer back to my record all the time. One good point of it is, you required minimal knowledge programming to configure this as that's probably why you are paying for it, unlike Cell Profiler Analyst. It is also linked with sportfire decision that enable you to develop a report once the analysis is done, however I did not get to experience that so I could not give any further input of thought.

Anothe software I tried was Metamorph software by Molecular Devices, they did good job in scoring cells, but it gave me a report in excel, which was troublesome to a certain extend. However, I heard that they are coming out something for high throughput imaging, so the software would work better.

I am not an expert, I was lucky to have a chance to experience these softwares, but I did not get to fully cover the use of the whole software.

Hi, Image J is a good software for image analysis. It is free to download and you can find guide of this software in internet.

Hello Fiona,

ImageJ was already recommended several times. I do this again. For scientific researchers I would always recommend to use/download Fiji. Fiji is based on ImageJ (that's why it's called Fiji - Fiji Is Just ImageJ) where almost all available plugins for data analyses are already included and constantly updated. Furthermore, you can write very easily macros that will deal with your big data sets automatically. There are many easy-to-follow tutorials online. You can even record a macro automatically just by analysing an image once as a reference.

You will see that for your kind of analysis an expensive software package might not be necessary.

But if you want to spent some good money, I would suggest Imaris, since InCell Analyzer and Metamorph were already mentioned. You can get a quote on the corresponding website: http://www.bitplane.com/go/products/imaris/

The good thing about Imaris is that you can buy different software modules depending on what kind of analysis you want to perform. But the price might become and issue. Of course I don't know how much you could spent, but I received quotes ranging from 9 - 22k €.

I know this is a very old thread, but if you are still looking, I would defintely recommend you visit www.MIPAR.us. I think it would work perfectly for your needs.

It is very powerful and intuitive 2D/3D image analysis software written by scientists/end-users and is about to be released as a free trial on December 14th. You can sign up on the site as well as submit images/datasets to test.

There are many image analysis options available, but I think you may just find MIPAR to be something special if you give it a try!