The biggest difference that I see is that women are usually invited to parties. There is a huge gender imbalance in Japanese science research, and I think the culture around funding is responsible.
The funding in Japan flows through a senior researcher who organizes the research for an entire department. This is very different from the US where each PI applies to the funding agency (NSF, NIH...).
In 2010 I attended a department level conference (~75 people) in Japan and the the Japanese graduate students explained that when you meet with someone for a few days you get to know them and their research, and then when you go to the hot springs you really get to know them. After all of the formal sessions the organizer would say, "Ok, now lets all go to the hot springs and discuss what we heard today". Clothing is not permitted in these "baths".
The goal of the above post wasn't to make fun of the culture, but it does point out the system where friends of the lead researcher get a huge advantage.
This system is also very hostile to women who are unable to participate in the part of the meeting where the real business happens.
If anyone knows this to be untrue please let me know.