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Are there any rules for proper indentation in thesis?

I am physicist so my thesis includes number of images and equations.

Now I think you should not indent first paragraph after:

  • Title of chapter, section, subsection...

  • Image

  • Equation

Then you should follow the rule "One paragraph for one thought".

Is this right?

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    There are similar questions on this site. Many times it's easiest to ask if there is a style preference from the professor or if the professor can refer you to a model example. Otherwise, if you're really serious about it, invest in a style guide with scientific annotation. The Chicago Manual of Style is a good example. – Stu W Apr 23 '16 at 12:27
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Most universities have a style guide that you must follow when writing your thesis. When my wife wrote her thesis, she was required to follow the MLA style guide, which is where the rules for indentation and spacing, etc. are found.

I'd go to either your thesis committee or to your university's library to talk to somebody about the submission requirements. These are usually very strict, so knowing them in advance will save you much time later when it comes time to edit your thesis.

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In general, you would either use block format or full indentation for the whole paper. The only major exception would be the abstract, which is usually block format to save on characters.

Charles Lipson has a book entitled How to Write a BA Thesis, and Robert Day's How to Write and Publish a Scientific Paper has an index that should help. They are probably available in your library and can quickly answer individual questions.

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