Hi, Yulia, FM dyes (as di-cationic liphophilic molecules) are the best one. One of the problem with all membrane labeling (including FM4-64) is hypocotyl hydrophobic. Pre-incubation for some time in liquid may partially solve problem.
Please, have a look also here: https://opus.bibliothek.uni-wuerzburg.de/opus4-wuerzburg/frontdoor/deliver/index/docId/6512/file/035_1746_4811_8_28.pdf and http://onlinelibrary.wiley.com/doi/10.1002/9780470027318.a9350/abstract;jsessionid=8D0EDA56A13D5A784F529E76F14FD7E0.f02t04?userIsAuthenticated=false&deniedAccessCustomisedMessage=
Dear Taras, thank you for the suggestion! I will try to pre-incubate the seedlings in liquid 1/2 MS in Phytotron for 10-30 min and hope that it will help, since I just need to prove swelling. Thank you also for the paper, especially, for the data on LAURDAN microscopy. Best regards, Yuliya