Formatting a PhD thesis

So, you have finished the sciency bits of you PhD degree, that is great. But now, the really awful part starts - actually compressing all of that into a cohesive document, your thesis. In this little post, the actual rewriting I will not discuss, although this is a real challenge1). Instead I will discuss formatting.

Formatting is not so important in many countries; in Germany for instance, a physical thesis is typically printed as a simple A4 booklet, of which maybe 4 or 5 real-life copies will ever exist. But in some countries, like The Netherlands you need to make a real physical booklet, with a real ISBN, typically with a print run of 100-150 pieces, to hand out to family, friends, and possibly, future employers. Therefore, you are compelled to spent a little time on something you probably have little or no interest in - formatting of books.

You can of course pay someone to do it, but, if you want to do everything to do with your thesis yourself due to a misplaced feeling of pride, or because you have a do-it-yourself attitude, you will need to put some work in.

But fear not, for in this post I will discuss the LaTeX template I made for my thesis, which you can use! That way, you don't have to worry about the boring detail (too) much! Using the template you will still need to make executive decisions, but at least you have a cheat-sheet to check. The template is specifically intended for creating a thesis according to the rules of the university of Amsterdam, but should be easy to adapt to your own needs. If you don't know LaTeX, you can still use the template, but I am not going to lie, it is going to be a bit harder to get started. Find a different guide to installing latex first, and you can begin.

You will also still need to find or make a nice image for the cover; mine was drawn by my mother (see below).

You can check here what my thesis looks like to see if you (kinda) like it before you commit to using this template. But keep in mind you can really change a lot.

The template

This template is build on the excellent latex-mimosis template. Under the hood, latex-mimosis uses KOMA-script which is a huge package that provides alternatives to the standard LaTeX classes (like book, article, etc.) with many options. To use the template, download (or clone if you know git) this repository, paste in your text in each chapter, run LaTeX in the way you usually run it, and a nice thesis should come out!

However, this template is made for tinkering. I would strongly advise you to go through the explanation below and go through all settings files to set up everything to your liking, etc.

How this template works

The setting files

First, go over the setting files: mimosis.cls Contains the mimosis class. It does quite a few things, like loading certain packages and changing default settings here and there. It also sets up a font, so change that if you don’t like the one currently setup. For more information, see the latex-mimosis repository. In general it is better to not change this complicated file too much and use other setting files to get the desired results. However, don’t be afraid to change things and break stuff - if you feel like it, you can always return to the original state.


Load all packages. Note that quite a lot of packages are already loaded inside mimosis, so what you see here is not all the packages we use. For the packages’ mimosis uses, open mimosis.cls, and look for \RequirePackage commands. I tried to keep the settings of the imported packages separated from the file, but that is not always possible. It should be pretty well documented what each package does. Add stuff yourself if you want to.


Handle how you want to show your bibliography. This can get surprisingly complicated, so this dedicated file will contain all settings. I put my personal preferences there, feel free to change what you want. This template uses biblatex, which is just a way of handling citations most standard latex installations will support.


Here you can change all settings of the document. A lot of things are set up by default, go over them and decide if you agree.


Small definitions, like \com, which just colours text red, good for making comments. Also used to set hyphenation: especially personal names in the bibliography will stick out into the margin sometimes, using these settings you can break the names and make things look better.


Each chapter gets their own folder, containing chapterX.tex and a dedicated Figures folder where you can put figures belonging to the chapter. Each chapterX.tex file starts with some commands which make sure the chapter starts on the right page (left or right in the booklet), then has room to include a quote (optional), and an abstract (not optional), before the actual chapter starts. Just look at the examples, replace with your own text.

There is also a folder called preface, which contains .tex files which are part of the preface: the official title and committee pages (received from the office of the beadle), the colophon and anything else you want to put before the thesis really starts. I include a template for the pages the beadle gives you, where you can just replace your own name etc.

The postface folder similarly contains the texfiles related to the postface: acknowledgements, the list of publications, whatever else you want to put there.


In this template, each chapter gets its own theme colour (setup in mimosis-personal.tex). In the first bit of chapterX.tex files, I set up things such that the colour is used for all highlighted text. You can use the command \textcolor{\chapclr}{Your text here.} to set any of your text to the current theme colour.

Actually loading everything and outputting a document

The main.tex file is the main LaTeX file. Instead of putting text here directly, like you would in a ‘regular’ LaTeX document, this file is used to load settings and the individual chapters of your thesis. If you open up main.tex, you see it first loads the mimosis class. After that, it uses \input commands to load all settings and chapters. There are also some weird settings that change over the course of the booklet, hopefully the remainder of this readme make clear why.

What your thesis should look like (and when)

This bit is really only interesting if you are doing your PhD in the Netherlands, and it is especially aimed at Amsterdam, but I got confused about it all the time, so I wrote this down, maybe it helps someone at some point.

Section to include

Although we typically think of a PhD thesis only in its completed form, there are actually 2 different versions. This is explained in the thesis regulations of your university, for the University of Amsterdam, you can find that here.

  1. A first ‘reading’ version of the thesis. This needs to be turned in with your PhD committee, several weeks before the planned date of your defense (at UvA, its 14 weeks, so a long time!). This version MUST contain all scientific content (so your chapters, bibliography, etc.). No one will ever see this version, except for your (co-)promotors and the committee. It is only digital. Apart from the scientific content, the reading version must contain the following:
    • All figures, tables, etc.
    • Table of contents.
    • Acknowledgement of financial support of research.
    • If the thesis consists of an article or articles in the name of several authors: a page with a complete reference list with a list of authors for each article and an explanation of the relative importance of the co-authors.
    • A summary.
    • A bibliography.
  2. A ‘final’ version. After the committee approves the ‘reading’ version of your thesis, you prepare this version. The scientific content of the final version is identical to the reading version (no changes! Even grammatical corrections are banned, only spelling errors can be fixed). Apart from the contents of the reading version of the thesis, the following are added:
    • A nice cover. This is not actually relevant for the pdf you will generate.
    • A title page, as given by the office of the beadle (‘pedel’) (this is mandatory).
    • Colophon (a page with the ISBN, credits for the design of the cover, etc.).
    • Layout changes.
    • A summary in your own language, typically aimed at laymen (i.e., your parents).
    • An acknowledgement section.

In this template you can just turn sections you don’t need on and off, meaning that you can prepare the reading and final version of your thesis at the same time.

Digital vs printed versions

Dutch PhD theses are always printed as a 17x24cm booklet. Since this is a weird size, it may be tempting to just submit your reading version to the committee in A4 size. This is a mistake! Figures and tables will shrink significantly when changing over to the smaller paper size of the final version, meaning you may not be able to read them in the final version of your thesis. Since you cannot change Figures after submitting the reading version, this means you are stuck with too small graphics.

However, you should also not send the reading version in exactly the same formatting as the final version: since the final version of your thesis will be a printed booklet, you need to adjust page margins and the like (this template can do this for you). This template makes it easy to switch between generating pdfs suitable for reading on a PC and pdfs suitable for the printing press.

Boring details about page ordering and typography

This may explain some seemingly odd choices of commands


To print a booklet, you actually cut the pages out of a bigger piece of paper. This is never 100% exact, so you add ‘bleed’, just a little bit of extra space to the edges of your page, to prevent white rims around an image or line that reaches the end of the page. The printer will tell you what the minimum bleed is, typically 2-5 mm on all sides. A package is included to add this bleed, it is not nessecary for the regular reading version.

Coverpages and titlepages

In printed books, it is normal to include a cover page before the ‘real’ titlepage, so we do that as well in the thesis! If you open your booklet, on the left side, you have the inside of your cover, on the right side the cover page, just containing a title and your name. On the next page, there is an empty page on the left, and on the right, the thesis really starts with the official tile page. To make this work you have to be careful that page numbering starts at the right place, this template currently does that correctly.

Empty pages and where they live

By default, each chapter always starts on a right-hand page. This is pretty normal in printed books. If a previous page ends on a left-hand page, the chapter starts immediately next to that. We control this behaviour with \KOMAoptions{open=right}.

However, I don’t like this title page on the right, with the previous chapter on the left: in my own thesis, I wanted to put a picture at the left-hand side, relevant to the chapter starting on the right. So, in this template at every chapter I insert \cleardoubleevenemptypage to skip to the first right-handed page before inserting the chapter heading, leading to the desired behaviour. This behaviour is explained in the KOMA-script docs, section 3.13.

Please note that changes in the \cleardoubleevenemptypage and \KOMAoptions{open=right} commands can have pretty weird effects that are not always easy to sort out, so be a bit careful if you want to change those things.

If you (like me) want to add a picture on the left empty page, which might be nice, insert before the beginning of the rest of the chapter the following:

\chapter{Just an example chapter}
% ... the rest of the chapter .... %

And tada, a picture will show left, the chapter begins on the right. Note the width parameter, it sets the size of the image. Make it wide enough; the bleed must be included or you may get a weird white border around the image.

I spent a week debating whether to use the “scientific” we, or do you switch to I? Or do you vary throughout the document?


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