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The formant spectrogram in this page points F1 and F2 as below;

enter image description here

In bottom-right F1 movement, I thought F1 could be below blue one. But how can we determine F1 is upper one not below one?

enter image description here

Is it because we know F1 and F2 have to be getting closer from [ε] to [ae]? Or, can we determine F1 only with spectrogram?

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    $\begingroup$ Can I please ask you to edit the question for clarity? I am not really sure that I understand the question but that could be just me. Have you looked into the topic of formant tracking? $\endgroup$ – A_A Nov 18 '17 at 10:21
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You should be able to see formants very clearly as peaks on the spectrogram slices. The 1st, 2nd ... are the several peaks. In the picture above (in the blue area) the first two peaks seem to have very similar power and so this can introduce errors in the estimation algorithm.

You can use Praat and "Show formants" option to track formants and observe their behaviour over time. You can try to make continuous transitions from vowel to vowel and then try the same vowels with a silence in the middle and observe the differences.

If you are developing an algorithm you can use a Kalman filter for tracking formants. (maybe this helps: http://link.springer.com/content/pdf/10.1007/978-3-540-85980-2.pdf#page=257)

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