The Imaris Guy - Synaptic_Pairing9 - Find Your Match
Hello World....again!!!! Welcome to the inaugural launch of TheImarisGuy newsletter!!! As I continue to create content, I am trying to find my voice in the online world and trying to find the best way to find my audience. Most of the videos I create are primarily designed for those already familiar with Imaris. I hope to introduce new scientists to some tools that they may be interested in, as well.
This XTension came directly from conversations with people that wished to expand the definition of colocalization, especially between pre- and post-synaptic puncta. Instead of just the number of colocalized spots, they wanted to see if there was more to it. This could be particularly interesting for neurodegenerative models where there is an expected loss of synaptic connections. This could also be used in many other scenarios.
As with most of my advanced analysis XTensions, they are works in progress, including this one (always keep an eye on the version number). Plus, if you are interested, please send me comments about how to make it better or what to do add. Stay tuned to updates, which hopefully I will post here when they happen. You may ask, why am I including this in my inaugural newsletter??? Well, being a neuroscientist myself, out of all the programs I have used in my career, I have not seen an analysis do what this XTension does.
WalkThrough -- XT_MJG_SYNAPTIC_PAIRING9
Required Python3.7 Libraries:
numpy, scipy
Description:
Colocalization between 2 sets of Spots objects as measured by the closet distance between spot centers. Threshold is set by the end user in dialog box.
Work in progress...A custom statistic is generated for each set of paired spots This custom statistic will act like a ColocID between the Spots objects. So you can identify which spot is linked to its partner. This seems to be working for the singlet spots, but others are not quite matching up, yet.
Types of colocalization identified
Singlets - one spot colocalized with one spot
Doublets - two spots colocalized with one spot
Doublets Special - doublet and single (describe in video)
Triplets - three spots colocalized with one spot
Quadruplets - four spots colocalized with one spot