All-around the program is a breeze to use, and does a fantastic job of automatically tracing through a stack of confocal images based on the fluorescence intensity. It has manual, semi-manual, and automatic tracing modes for complete 3D reconstruction. It has a comprehensive help manual that will walk you through everything you need to know. Don’t be thrown by the lack of updates since 2009 or the fact that you need Windows 2000/XP/Vista to run it. If you need to trace the dendritic arbor of a neuron then this is by far the best free open source program that I came across. Neuronstudio – Automatic Neuron Tracing Super-Tool

Give it a try and let me know what you think.ģ. I’ve never used Cell Analyst but I’ve heard good things about its ability to handle large datasets. It’s as simple as setting up your pipeline and then going for a coffee. It can quantify antibody fluorescence intensity, colocalization, cell density, or even track cells through time-lapse movies. Cell Profiler/Cell Analyst – Image Batch Processing and Data AnalysisĬell Profiler can extract quantitative measurements from thousands of images through a custom pipeline that can first process and then analyze your images. The select grouping of plugins is geared for neuroscience.Ģ. There were a few plugins that were only available in FIJI. Downloading FIJI instead of ImageJ just starts you out with more base plugins so you don’t have to hunt around and add them to your ImageJ program. It can also easily handle 3D stacks of confocal microscopy images, and perform complex quantitative analysis.įor more information visit their website: įIJI (FIJI Is Just ImageJ) is a bundle of the top plugins available for ImageJ. It can do simple things like crop, label, and alter the brightness and contrast of fluorescence images. Being proficient at using ImageJ is essential for most image processing and analysis. Download it, search through the plugins to see what’s available and test them out. ImageJ should be the first program you become familiar with when looking for image analysis software. Here are my Top 5 favorite time/life savers: It took me years (actually!) to find some of them, so I thought I would pay-it-forward by sharing them with you! Kudos to everyone who takes the time to create these free open source programs.

Out of sheer necessity to analyze a massive image set before I turned grey, I scrounged around for free open source software programs to help analyze my confocal microscopy image stacks. If your lab was like mine was, you struggle to afford new antibodies, let alone expensive image analysis software programs like Neurolucida to analyze your data.

Commercialization/Collaboration Program.Neurodegenerative Protein Handling Instructions.Active Pre-formed Fibrils for Neurodegeneration Research.

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