I have a game ending soon with seki under Japanese ruleset. When I do score estimate, my white three stones surrounded by black but in Seki situation are marked as black. I am wondering what the picture looks like in final score and if there is any concern to just blindly accept auto score result.
I mean I know how to verify the other part of auto score result, but am not sure about the Seki area.
I expect its possible that autoscore makes a mistake handling seki. I dont know of any method to correct autoscore other than clicking the stones involved if thats what you mean?
it should be possible to mark all stones (black and white) as alive.
You can mark the eyes in seki as neutral as well by clicking on them.
In other words, if i my live stones under seki are marked as white, my color, I can trust the system?
The score is calculated by counting all points marked by colored squares. You can trust the system to be able to sum correctly.
But you have to check if the assignment of stones alive/dead and neutral points is correct.
Especially eyes of groups in seki can be difficult to get right (by a program).
got it. thanks. luckily in this instance, there is no eye shape, just three straight stones surrounded. i just need to make sure the two extra spaces in seki are marked as dames and stones are marked as their own colors.
I wish the auto score shows me the result when asking me to accept, then i would always know when to accept, aka, when i win. 
For the record, the game finished. The auto score did not recognize the seki and my opponent had to manually marked my surrounded stones as live.
It seems you figured it all out, but yes, some types of seki can still confuse our auto-score big time 
And it pretty much does (just not in an obvious way) before accepting a result current marked points for both players are displayed below their names. You can quickly compare them to see which is bigger.