I tried mitotracker staining by adding different concentrations of mitotracker to the zf embryo medium. But the penetration towards the inner organs seems inefficient.
Hi, I suggest you to give up with this strategy. The only way to label mitochondria is, in my opinion, through the injection of plasmids encoding for fluorescent probes targeted to mitochondria. I've been working for three years with zebrafish mitochondria, and this is the best way I found. Mitotracker is inefficient to penetrate tissues deeper then skin.
Domenico Cieri could you give some references about the difficulties you undergo in mitotracker assay for zebrafish embryos. Have you seen does problems in early embryo stages to?