Learned about #Mastadon this week from the bird app & fell in love, so prob good to join in for #FollowFriday. I'm a neurobio postdoc w/ a mechE background doing a lot of calcium imaging & analysis in Python and ImageJ. I also ride bikes, a lot. Probably too much if you ask my academic mentors.
A few rad ppl to follow:
@Russpoldrack
@weinberz
@SherlockpHolmes
@PracheeAC
I read that Mastadon is more interactive than bird app & I'm looking for ppl to follow, so maybe say hello if that's you?
@engineeringjoy @Russpoldrack @weinberz @SherlockpHolmes @PracheeAC Welcome fellow #ImageJ -er. Curious about Ca2+ analysis: does it run within ImageJ (or #FijiSc?) and if so which plugin do you use?
@engineeringjoy A nice example for the use of caiman (which was dropped in later versions because we didn’t need it necessarily, but you can scroll through earlier commits) is an analysis pipeline for Ca2+ imaging in beta cells. It is used on regular basis on our analysis server. Code is discoverable at: https://github.com/szarma/Physio_Ca
I also just noticed you’re working in flies. Tom Clandinin (not on social media) at Stanford may have good suggestions. He’s doing some cool whole brain stuff and I think is building an open project (if I’m remembering correctly from the last talk of his that I saw).
Hi Albert! I’m working on a pipeline in Python using Cellpose for segmentation and then a lot of dataframe wrangling for analysis, quantification, etc. I want to see if I can use the Python tools called CaImAn but needed to port my pipeline over from ImageJ macros first. It’s one photon data from calcium indicator dyes from cells in culture so not exactly what a lot of existing tools are made for (e.g., I have to do quality control filtering based on dye loading or things like cell health)