a little bit of everything

Author: lesolorzanov Page 1 of 2

Why is there such bad mental health in academia?

This is a topic you see often in media, everyone who is studying struggles with at least one from: depression, sense of inferiority, anxiety, impostor syndrome, sense of inadequacy.

I argue that to problem comes all the way from school, to the moment you become a PI or a fellow, and all the systems that leech from science and human endeavor, like publishers.

When I started my CS bachelor, I was one of the lucky few in my country who had a good enough education to sort of tackle the challenge of the program. So when starting a bachelor program, many people are not ready, not in age, not in knowledge, not in discipline, not economically. During that period you need to already fight against the current. No to mention lack of mentorship and, in some places, an unstructured program full of half baked PhDs teaching the subjects sub-optimally and students hacking the grades instead of reading and learning.


In the master studies, no one takes you seriously, lack of mentorship is still there, people higher up are either too busy or too uninterested. You are perhaps not ready to face the program academically, also there are economical difficulties.


Then after a master (or two) finally comes the PhD. People start taking you a bit more seriously but not too much. By now you are supposed to know so many things, but if you accumulated “errors” in the previous years, there is a lot you have to learn. You need to learn what you didn’t before, plus new courses, develop projects, write papers and a thesis. If you are lucky, those papers will be supported by your PI. But if you are unlucky they can even get them stolen by the PI and friends, because you are “only” a PhD student. PhD students spend long days in labs, with samples, or in offices writing code or running all the statistics.


Then if you manage to finish the PhD, people take you finally seriously but you lack the ability of securing funding, so you are still not important and don’t have a say. Probably you are also very tired of something of a decade or more of this struggle. There is always a fight for resources, inefficient processes that you can’t change. The publishers and journals expect you to do all the work for free. You experiment, you do, you write, you pay, you review other scientist’s work and they get to reap the benefit, the publishers I mean. They milk you from all you have. Scientists are treated like “content creators”, who are paid in exposure and glory. But as a popular IG sound says: “exposure doesn’t pay the bills”, and only a well played fame gets you enough grants to keep on going.

When you become a PI or fellow you actually stop doing science. You suffer writing grants, one out of ten is accepted. With that money you need to hire people who are in the situation I just described, so forget about being lucky to get that one genius, they exist but they are black swans (rare events). So you are stuck with a dream, depressed unmotivated workers, a constant fight for funding and predatory publishers and spam who drown you with noise. In some places, you have no help with bureaucracy so you are your own secretary and you have very little time for anything else, even your family suffers.

So all along the way, many people are tired, lacking mentorship, they are not taught in context and it’s just repetition and brute force. The will and the excitement are drilled out from them along the way.

So what do we do?

If you are a young starting student, don’t hack your grades, you don’t know the harm you are doing to yourself. It’s difficult to be passionate about everything, but if you have talents an abilities, develop them by reading, be curious, ask. Nowadays there are many social media places where you can ask, so if you don’t have mentorship available in your university ask, don’t be shy, no one should shame you for wanting to learn and be better.

If you are a master student, choose your topic carefully, if it is going to be a long way to the top you might as well work on something you enjoy. You can’t and shouldn’t work alone, search for labs or groups around the world (don’t be confined to your country). Search that the labs and groups are good, look at their published work (and on ArXives), look at the profiles of the PI’s and people who work there.

If you are a PhD student, don’t fight the fact that you have to level up, you will have to read. If you are not used to reading and writing then probably a PhD is not for you. Having a master is already a good feat for industry which also has higher salaries and you can work on something more rewarding for you. But if you are up to the task, search for knowledge in a sea of information is not easy. Look at indexes and search engines. Like SCOPUS, Web of Science, Google Scholar, go to university libraries and their seminars on research methodologies. If you find good papers, look at the references. There are also good books, find them.

If you are a PI or fellow with people under your charge, maybe learning about leadership doesn’t hurt. If you hired people, don’t discriminate them or make their lives harder, don’t look at gender or race, judge only by their work and offer opportunities for training. Encourage those who have been with you for a longer time in your team to help the juniors and newcomers. You might want to make peace with the fact that there will be less hands-on work for you in the experiments, but if you are not happy at all with this, then even if you work closer to the science you will for sure need help with the management of your group, resources and information.

If you don’t like science, don’t like research, don’t like to read or write, then maybe academia is not for you, no matter what your parents or relatives or friends say putting pressure on you. If you choose this path under pressure it is unlikely you will succeed or be satisfied with it (not impossible, but unlikely).

What do you think? Are you ready to come to the Ivory tower?

Advice for fellow women

Some people don’t care, or even worse, don’t believe there is discrimination against women. So I left this part for the end in case some don’t want to read. But there is discrimination, in many dosages.

In a documentary about women in science, one of the main interviewees, says that she is tired and that she didn’t want to be forced to fight in the first place. Why does it have to be so hard? To work twice as much for the same reward? To have to prove yourself at every corner?

How much discrimination you will face today after 2022, will depend on the place you work, your country of origin, the country of origin of your co-workers, your starting knowledge, your ability to work in a group, your language (if its mother tongue or second one), your domain of knowledge.

My advice is, pay attention to how many women are involved or related in the groups you work, and if there are none, it can be that the filed is still inaccessible to women, the group is not necessarily to blame, but look at how women are treated in that group, be it during an interview or how many are cited in the papers they produce.

Don’t make it harder for other women or think less of them if they don’t seem to know what you do. We are all in an interdisciplinary world, people have different sets of skills. Learn and support each other. It is very satisfactory to grow together, do it, experience it for yourself, chances are that women in your field have also struggled and I, personally, welcome the camaraderie as opposed to the competition.

Do not be afraid to voice your opinion and knowledge if something is incorrect. Show no fear, don’t let anyone smell it. Improve your confidence, if you are smart you have nothing to fear.

Connect and contact with other women, read their experience, nowadays there are so many groups in social media. You can contact them or join and just start the talk.

Men are not the enemy. Even if you have been put down, just don’t do it to others, it will pay off. If you happen to get power don’t get greedy trying to put others down, set an example. There are just a few trolls, that can destroy others with one ugly comment amidst and ocean of nice feedback and constructive criticisms, don’t pay attention to them.

Presentación en mi alma mater

Durante 5 gloriosos años estudié mi carrera de Ingeniería de Sistemas en la Universidad Nacional de Colombia. No solo aprendí matemáticas y computación también aprendí sobre mi país y viví muchas experiencias únicas y conocí personas maravillosas.

Mi profesor de métodos numéricos: Francisco Gomez, me dió la oportunidad de presentar mi trabajo antes un grán público de estudiantes en la UNAL, lo cual fue para mi casi un sueño, ya que siempre había querido volver y mostrar algo de lo que he hecho desde que me gradué.

No había escrito nada en español antes por que se que si nadie lee en inglés, menos van a leer en español. jaja. Pero aquí va, el video de la presentación para los que se lo perdieron.

Y estos son de otra presentación pero son bonitos ;P

Curriculum Vitae

Since this is my website and I can write whatever I want, and few loving people will read it, I wanted to write about my latest CV and what it contains more in detail.

Page 1

Here’s my main info. About my education, bachelor, masters x2, and PhD. I also wanted to show selected publications since this is an important aspect of my career so far. Publications are almost a currency in academy, and whether I continue in academy or not, these works show that I am a researcher and that I like to write, create and solve problems. Additionally I show contact details, skills in many areas and languages, human ones at least.

Long ago in 2007 I started the way to a 5 year bachelor program that is so good that it is equivalent to European program where people do 3+2 years and while they end up as “masters” I was still considered a bachelor. Then I started my master in Colombia and before finished I was offered to start an M2 in France. After I finished that master I came back to finish the one in Colombia. This is why The road is displayed like this, I like to tell stories. Also it resembles the branching and merging of version control.

This is my favorite part of the CV. I took it from my thesis defense. All the aspects of being an image analyst and computer scientist and researcher are colorfully displayed in the bottom. Each of those aspects can be covered in the publications and I wanted to show which aspects could be found in each paper, I love this idea I had to basically summarize the paper in a small image. Additionally on the side there is a square containing the type of microscopy image used. Microscopy is an enormous and beautiful field where many different modalities are used.

This is my tool belt. In order to do what I do, a lot of magic is needed. I speak human and computer languages. I also learned how to use the frameworks for Artificial Intelligence but most specifically PyTorch and Scikit-Learn. I use Pandas to store and process my data and I also know how to use MySQl databases although I prefer NoSQL databases like MongoDB. I use, love and promote Linux but I also work on Windows if necessary. As you may know I love and use Blender for everything. I also use other visualization tools like D3 and Seaborn. It’s safe to say I know how to use a lot more software and tools but I haven’t used them professionally or at work but I am a box of surprises.

Finally, easy, the languages. My native language is Spanish but I think one doesn’t ever discover all the wonderful things about a language which is why I leave a little part uncovered. The same for English, I have used it all my life but I am not a native. My impostor syndrome tells me I know less french than I do but the proof is that I lived in France and I studied a master in the language so I must know enough to have managed that at least. I am learning Swedish and it has been a difficult language because I don’t have time anymore, doing a PhD was tough and I had little time but I tried, on my own and with friends and now I finally have time and money to pay for a small group course.

All other pages

Since I will apply to academic positions I need to have a list of publications which is page 2. I add all my other Academic experience in page 3 and work experience in page 4 and since It was a bit white and cold and lonely I put the art I made for my thesis which is quite nice, if I may say so myself.

How to

I have been asked to explain how I do my illustrations and how the whole process goes. So here are some tips. For insights about visualization in general read the last chapter of my thesis, it’s quite short and nicely summarizes everything I think about visualization. I might write a post about it.

I use Inkscape, I only use free and open source tools. Inkscape is a fantastic software for vector graphics and I do all my posters and figures in it, along with GIMP and Blender. I use a lot of shortcuts and I’m quite efficient.

The tools I use the most are:

Fill and stroke
Align
Transformations

and of course Selection and edit paths by nodes. I really recommend learning key shortcuts. If you want to learn how to use Inkscape let me know. We can talk about it.

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

Posters in Image Analysis for Microscopy

Through my PhD I had the wonderful opportunity of traveling to different countries to learn and to show my work. It was a very exciting time and I put all my skills in design to the test. In this post I want to share with you the posters I did and talk a little bit about them.

I do all my posters and figures in Inkscape, Blender and GIMP, all free and open source software for design that have all the same tools as private paid software. I also program a lot of the SVG figures using javascript and D3,

Exploratory analysis and visualization of in-situ sequencing data

TissUUmaps a tool to explore millions of points of in-situ sequencing data directly on top of the tissue. Offline or online, with documentation, you can use the browser console to analyze using javascript or simply use the GUI. Presented in EMBL – Seeing is believing as a lightning talk and in Janelia’s Women in Computational Biology conference in the U.S.

Learning from the interaction of gene expression, protein expression and tissue morphology, to make better decision about cancer treatment

In the group where I worked we are very interested in combining different sources of information and use spatial information to analyze and visualize biological phenomena. Presented at a Deep Learning workshop at the Center for Systems Biology in Dresden.

Quality Assurance and Local Regions for Whole Slide Image Registration

When trying to align WSI it is hard to evaluate and also to find out relevant locations. This poster shows how I approach this problem and gives some fun facts about WSI. I presented it in the European Congress of Digital Pathology.

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 🙂

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 Öfverstedt.
  • 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 Wählby 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.

Nataša 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

Recreate your city in 3D with Blender

In one of my personal projects I wanted to see Uppsala, the city I live in, in 3D. Those who know me know I am a Blenderhead, a Blender die hard fan for reasons I will discuss at some time. But now, how can yo do it by yourself with your own city?

Warning, I actually had to remodel the Cathedral

This was really hard to find, specially open, but I love open stuff and there is OpenStreetmap where you can export an OSM (openstreetmap) file which is some sort of XML file with a lot of information, including where trees and buildings are.

To export a place go to OpenStreetMap and explore, then click export and you will get the longitude and latitude borders of your area. If the area is to big you will have a very big file! obviously! so be careful.

After you get your OSM file you need to convert it to something to open on Blender.

Some german hero created a software called osm2world that can convert OSM to OBJ which is a format that Blender can open. I found it a tad difficult to use but it’s amazing that it has java executables for any operative system, mine is Linux (obviously).

I run it in a console using

java -Xmx2G -jar OSM2World.jar -i input.osm -o output.obj

And it’s as easy as that now you have an OBJ that you can open in Blender like this:

But of course it is not all puppies and rainbows, buildings might not be perfectly modeled and color can be lost, and there is a clutter of things that I didn’t want to see, I don’t care about little benches or traffic lights and many more things that were not correctly placed, not correctly modeled and don’t really add much since I won’t be visiting with that level of detail. I just wanted a panoramic view.

So how do you get rid of all these things? depending on how big of an area you exported, you might get different amount of things, maybe you don’t need to clean. But I did and I will show you how and if you want to do it too, I will give you my code.

What is OBJ

Wavefront .OBJ is a way to save meshes (vertices, edges, faces and color) in plain text, you can open it in a text editor and see what is inside. You can group vertices and edges and name these groups as something recognizable, that you could delete. But given the organization of the file you can’t just delete the text you have to rearrange all the vertices and edges and faces which was an absolute nightmare for me.

Wonderful people who believe in open source create software every now and then that can do things like this, but sometimes they are overkill for a small task, sometimes they don’t work as you intended and I am all up for programming my own things, be them complex or simple. So I made a script that finds all objects, removes all the undesired objects by name and then rearranges all the vertices again and produces a clean OBJ to import in Blender. Mind you, it’s not perfect and could be better but it worked for my purposes so that’s the end of it. You can find the code here.

So now can I see my city please? Yes sure, here it is, ugly buildings and all.

This is NOT what the Uppsala Cathedral looks like

Playing with Blender and architecture

I will not be teaching you Blender here but if you invite me a coffee I might tell you about it. How ever if you are not seeing all your city it might be that you need to expand your view in Blender if the city is too big you can do this in a menu that appears pressing N or by dragging a little cross in the upper right side of the viewport, here you can select to clip the view at a larger distance.

So to model the cathedral (which was a hard task) I wanted to find real blueprints of the building and it was tough because I had to do ti in swedish (which I do not yet master) but a friend helped me by giving me some tips. She works in digital humanities so she knows her stuff.

She told me to search in ALVIN which is a platform for digital collections and digitized cultural heritage. I searched in Alvin and in google for the words

Uppsala domkyrka, domkyrkoarkitekt, ritning, planritning

And eventually found some good examples:

References for modelling the Domkyrka

So my recommendation becomes to know where to search for blueprints and historical archives and speak the language of where you are searching history from.

Anyways, I played with the depth of field with the f-stop the focal length and placing the camera around and with a simple white material on everything I made these two things.

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