I have a user who is growing organoids in matrigel. They then want to stain and image them. However, they find that the matrigel produces a lot of background. Has anyone encountered this, and if so, how did you overcome it? My fist thought is for them to completely dissociate the fixed organoids from the matrigel and then spin them onto PLL or ConA coated glass surfaces.
There are many matrices that can be used for oranoids, spheroids, etc., if they need Matrigel then they’ll have to dead with it. What is the nature of the autofluorescence, is it glow from the gel itself, in all channels. is it medium trapped in the gel? In the past, at least for spheroids (not organoids), I used a product called Qgel, which was very optically transparent and had (apparently) very little autoflurescence, could image through hundreds of microns using normal scanning confocal.
What media are they using when they make the Matrigel?
I think it’s standard media (I’ll check). They’re evidently getting fluorescence in all of the channels. I might recommend for them to use NaBH4 to try to quench the fluorescence and see if this improves things.