a little bit of everything

Category: PhD

I am a jack of all trades

and it is ok

All my life I have been exploring knowledge. I was in a good school, learned so many aspects about the world, life and everything (42). It’s always been my fascination, to keep learning and understanding and connecting concepts ogether to form new knowledge and answer questions that have not been answered before. Even to ask questions never asked before. This is because today I am a fully formed researcher.

Nevertheless I have always struggled with a sense of inadequacy. I feel I don’t know enough, about anything. This is called or is part of the impostor syndrome. I feel like an impostor, but a bachelor degree, two masters and a PhD might indicate I must know something about something!

Sometime ago I saw a very interesting description of what a PhD is, by Matt Might, called The illustrated guide to a Ph.D. He illustrates all knowledge as a circle. When you finish school your knowledge is around the blue and green parts. Then you get a bachelor degree, the orange part, and then you get a master to specialize in an area which is the protrusion in the illustration. When you “zoom in” and specialize a bit more, you are effectively pushing further this boundary of knowledge and you have invented something new. A tiny little nudge to the border, that is the PhD.

Illustration by Matt Might

In my country, arguably, knowledge is not appreciated and there is a love/hate (or more of a love to hate) relationship towards people who achieve any kind of academic degree. Such people are more often than not, admired and hated. This view makes it so that one sees one’s own academic achievement as more grandiose. Regardless, being a PhD means you went through a lot and you have to keep learning and applying your knowledge in real life problems. This all makes it so, that you see your own PhD from a very “zoomed in” and limited perspective. But it’s important to remain humble and face the reality that your little bubble is a but a tiny aspect of all knowledge humanity has collected.

Illustration by Matt Might, I added the caption

The thing is, by now, I feel my circle of knowledge looks more like this:

A narrower long protrusion towards my PhD and a whole bunch of other knowledge, some in which I did masters and some of which I just wanted so much to know about that I have invested a lot of time to learn it.

So. I would say I am your typical nerd. I rather study than go out. I rather discuss deep subjects than shallow. I rather understand a topic deeply and be involved in projects than have an overview. This caused me to learn about a lot of things but with limited time and resources, I can only devote my self to so many things and so much depth.

And you know what? I like it and it is ok. This means I can have a conversation with a broader population, I empathize with the struggles they go through learning. I can connect my main knowledge (whatever that is) to their fields so I can talk to them and help them or simply have fun together.

But it has also caused me difficulties. When I am asked to narrow down, or to specialize, or when I am looking for a job, I don’t know what exactly I want, what exactly am I really good for, and where I can really shine and help and be very efficient, these are questions jack of all trades ask themselves.

I am a computer scientist and engineer. When I was pondering a road to follow I chose between medicine and CS. So I went with CS but ended up using a lot of my knowledge in many medical questions for more than a decade now. But I also like videogames, and I always wanted to know about how to make them, not only programming but the concepts and the art and the engines. So along with programming come algorithms, and that field is all over, in all areas, all of you have problems that need solving, I want to solve them efficiently, and solving them efficiently requires algorithms. I also learned about art and design and that led me to both the artistic side of art (forgive my redundancy) and the mathematical side.

So I understand how computers and hardware is built, I understand how they work, how to program them to do whatever I want. And what I have wanted all through my life has been around so many areas of knowledge that I am so tired. I have learned about medicine and biology, I have learned about computer graphics, image and signal processing. I have learned geometry. I have learned about graphic design. I have learned about data analysis and visualization. I have learned about software engineering and good practices. I have learned about Machine Learning. I have learned about 3D, in math and in design. And all of them I have applied or used one way or another using a myriad of available technologies.

I am also interested in things outside science and technology. I sculpt, I like cinema, I like music, I like to understand how societies work, how personal relationships work.

And within all the things I have studied, and all the things I have done as a hobby, there are internal topics and divisions. To give you a “small” example, I love Blender, the 3D software. With it you can model objects, sculpt, rigg, animate, track, video edit, paint, and now you can even do 2D design. That is only from the artistic side. Underneath the enormous powerful beast are 7512342 lines of code, out of which 5228590 are in C, 1577591 are in C++, 465765 are in python, 82635 are in GLSL and the rest in more languages. I wish had not given up on C++, I might return to it one day.

So even when I have been playing around with Blender for like 10 years, I can barely model things and maybe sculpt and maybe animate a few things here and there. But those I do quite ok.

The same thing goes for everything. I know quite some biology of tissue due to my long PhD protrusion, and I know how to analyze images and find cells in them and I know how to teach a computer to find things for me and help me help the bio-person answer their questions from hundreds, thousands or millions of samples.

I know how to design beautiful things, by hand or by code. I know how to make an impactful poster but also how to display information dynamically on some process.

I like to make websites and interactive experiences.

I like to automate everything I can automate.

I like to tinker with electronics (although this is admittedly less well done).

I learn languages and to study them with and without technology

I know how to manage projects and technology projects.

I like to analyze signals and understand how our senses work, both sound and smell.

And for more thoughts on being a jack of all trades and many more topics:

Being a jack of all trades in Blender

To learn 2D in Blender

To learn more about design in bio informatics

Memories of the thesis defense day

The day is May 12th 2021. Location: The magnificent Universitetshuset or main university building at Uppsala University, a place where Nobel price winners and nominees gather to have dinner and discuss.

Universitetshuset – Image by University Press

Due to the world situation with COVID, only 8 people are allowed in the auditorium, but it’s enough to make me feel happy and supported.

The speaker stand is adorned by a beautiful golden emblem of the university and this time it was my time to speak. I feel important!

Here is a video of my presentation. If you want to read the thesis you can find it here.

Image Processing, Machine Learning and Visualization for Tissue Analysis – Pop science presentation at Sal IX, Universitetshuset, Uppsala University

The whole event lasted some 5 hours, but I can only share publicly my part of the presentation.

I received very good and detailed questions and debate about my work which is always encouraging so I am very thankful to the opponent and the committee.

After a closed door deliberation, committee member, Prof. Anna Kreshuk announced that they were pleased with my answers and that they agreed I should be granted my title of Teknologie doktor (Doctor of Philosophy in English).

My supervisor Carolina Wählby had many surprises for me! Along with my boyfriend and friends and colleagues I received much love, many gifts and flowers and we enjoyed a fun moment playing a quiz about me! It was really funny and had many tricky questions!

Summer started the very same day and in the end a few of us had a corona-safe picnic right in front of Universitetshuset. It was a perfect day! Quite the fairy tale finish!

One of the gifts included a driving lesson gift card, so I guess that now I really have to learn. So many adventures to come! I look forward to whatever comes my way!

Invitation to thesis defense

On May 12th 2021, 13:00 Uppsala time, I will be defending my thesis. Four and half years of hard work summarized that day. I hope to get interesting questions and debate.


Link to opponent and committee discussion. Password protected. For Opponent and committee members only!
https://uu-se.zoom.us/j/62405671377

Want to say hello or wish me good luck? Leave a comment and it will be a guest book ūüôā

Thesis document

You can find the document here. I presented all my papers and thesis in a previous post here.

What to expect?

  • This kind of event can last many hours. Plan for it, grab coffee and dinner.
  • We start at 13:00 in Uppsala time, for other times in the world see here.
  • I will give a 20 minute popular science presentation, followed by a talk by the opponent which is much longer and then questions and debate with the committee.
  • Please mute your microphones and cameras. They will not be allowed anyways. After the presentation and defense, while the committee deliberates we can all stick around and chat.
  • In the end there might be the possibility for the audience to ask questions. Please use the “raise hand” option in zoom if you want to ask a question and please be respectful.
  • If you have any questions regarding¬†this zoom event write a private message on the zoom chat to the event manager: Johan √Ėfverstedt.
  • After deliberation we will all gather in the same original zoom link
  • I am thankful for all the words of love and encouragement from friends. But please refrain from using the chat to “say hello”. We will all be able to talk and communicate while the committee deliberates. Or you can leave a comment in this post.

Who is the committee?

We are glad and thankful to count with the presence of:

Opponent:

  • Alexandru Telea

Committee:

  • Bjoern Mentze
  • Anna Kreschuk
  • Caroline Gallant
  • Stefan Seipel
  • Patric Ljung

Supervisor

Carolina Wählby

Chair

Ingela Nyström

This is me

Wish me luck!

Sign the guestbook below :

Image Processing, Machine Learning and Visualization for Tissue Analysis

Digital Comprehensive Summaries of Uppsala Dissertations
from the Faculty of Science and Technology 2025

Main document

Image Processing, Machine Learning and Visualization for Tissue Analysis

See the version in Uppsala University’s DiVA portal

Accompanying papers

These are the papers where I am first author. They are published under an open access license with the exception of paper III.

Paper I

TissUUmaps: interactive visualization of large-scale spatial gene expression and tissue morphology data

At: Bioinformatics – Oxford University Press

Paper II

Towards Automatic Protein Co-Expression Quantification in Immunohistochemical TMA Slides

At: IEEE – Journal of Biomedical and Health Informatics

Paper III

Whole Slide Image Registration for the Study of Tumor Heterogeneity

At: MICCAI 2018 – Digital Pathology workshop

Paper IV

Machine learning for cell classification and neighborhood analysis in glioma tissue. (Under review)

At: BioRxiv preprint please note that this paper is being revised by us now and has improved greatly. We will make it available as soon as it is finished. you can find the revised version now.

Additional papers

These are publications where I also took part on as a supporting role.

Automated identification of the mouse brain’s spatial compartments from in situ sequencing data

At: BMC Biology

Artificial intelligence for diagnosis and grading of prostate cancer in biopsies: a population-based, diagnostic study

At: The Lancet – Oncology

Deep learning in image cytometry: a review

At: Cytometry part A

Transcriptome-Supervised Classification of Tissue Morphology UsingDeep Learning

At: IEEE International Symposium on Biomedical Imaging 2020

Decoding Gene Expression in 2D and 3D

At: Scandinavian Conference on Image Analysis 2017

You can see a full list of publications in my Google Scholar profile

My role models

I believe in equality, I believe everyone brings something to the table and that working together we can do much more. More and more people agree, but for my voice, and women’s voice to be listened to, so that we are all treated equal, many have fought difficult battles.

Many women fought so that I could have a better future as a woman.

As I grew up, I have surrounded myself with more and more women who have studied and work hard, really hard and are an inspiration for me. My best mentors have been my supervisors, my professors, in different parts of the world, and I want to talk to you about them today.

Carolina Wählby
PhD supervisor
Sweden
Marcela Hernandez
Master supervisor
Colombia
Claudia Jimenez
Professor in Big Data and Data Mining, Colombia

arolina W√§hlby is my PhD supervisor in Uppsala University and she has been the most amazing guide and tutor I have met. She has devoted her precious time to guide me and many more in the past and currently to become integral and honest researchers and she’s in the forefront of life sciences, she is helping the world understand the mechanisms of disease right in the RNA the smallest unit of us. She has the most impressive curriculum! She’s a member of the Royal Academy of Sciences in Sweden, and is a professor of many courses, has been awarded numerous grants and has seen many a PhD student start and then spread their wings and fly. She’s a member of so many comittees and groups that take important decisions. I can’t possibly name them all, that is why she has her own website and media. Not only Carolina works super hard in academia, she a wife and a mother of 3 and a scout mom. I honestly do not know how she manages. She’s my hero.

arcela Hernadez is my master supervisor. She gave me the chance to go to France and study in Lyon, where she herself did her master and went through very tough times. She’s a professor in image analysis in Andes University in Colombia and she’s a leader not only in computer science but also a champion of equal opportunities. Thanks to her I was able to fulfill my dreams and she keeps working and has worked very hard so that other women and other students also have better opportunities. She’s a marvelous example of work/life balance and I think I could never do what she does, and in Colombia on top of all, where there is a really long way to go to improve women’s inclusion in all fields and decisions.

laudia Jimenez is a professor in Big Data and is the coordinator of the Master of Information Engineering (MINE in spanish) in Andes University in Colombia. She was also a huge inspiration for me and I learned so much in her course that it made me really excited (I love to learn). In her course I really learned more deeply, formal methods for data analysis and for creating systems that can handle Big Data. During one lecture she said: “Those courses of Stanford and all U.S universities have nothing on us” and chuckled. But you know what? She was right. We’re always looked down upon, we’re the little guy, we’re women working in engineering in a country that loves to push women down to the middle ages. And yet she built herself a full master program in a prestigious university to give me and other women the opportunity to learn the bleeding edge technology that allows the internet to understand data. She included me in several interesting projects during my master and for that I am very grateful.

Sometimes I think I didn’t have enough mentors when I was young and I become sad. But later in life I managed to surround myself with great women, professors and classmates and all of them are all over the world participating in great things! and I want to mention them here.

I love you all, professors, sisters, mothers, friends. Even if some might not remember me, I remember them and what they taught me.

NataŇ°a Sladoje
Professor in Image Analysis,
Uppsala University
Ingela Nyström
Professor in visualization and image analysis in medicine
Uppsala University
Gunilla Borgefors
Professor Emeritus, Digital geoemtry and image analysis
Jenny Marcela Sanchez Torres
Professor in systems theory,
Universidad Nacional de Colombia
Saida Bouakaz
Professor in image analysis,
Université Claude Bernard de Lyon 1
Ida-Maria Sintorn
Senior lecturer in image analysis Uppsala University
All my colleagues of the computer science master in Colombia. They are now working all over the world in fantastic projects. Not only working but also being cool and creative and simply awesome.

There are so many important women in my life, my friends, my family and people I admire. From many universities, many countries, of all sizes and races and ages and all such a beautiful diverse group. I feel so happy to have met you all and I feel all your support, and I want you to know that you have my support.

And perhaps above all others, the woman who changed my life completely and who I love unconditionally and who loves me, my aunt Esperanza, who has taught me the beauties and wonders of the world before I went on my own to explore them.

Christmas 2010, Seattle, WA

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