a little bit of everything

Author: lesolorzanov Page 1 of 2

Academic traditions – doktorspromotionen

In academia, all over the world, the successful culmination of a PhD is celebrated socially in different ways. I’m lucky to have worked and received my diploma in Sweden, where the academic tradition of doktorspromotionen is followed.

Doktorspromotionen ceremony is a beautiful event where the promovendi (graduated PhDs) in technical fields (like me) participate in a Kransbindningsfest (The Feast of the Binding of the Laurel Crowns) and receive a beautiful diploma with a ribbon.

After the ceremony, a banquet is held in the evening, with long dresses, and tail coats. The banquet also has live music and interesting shows. I will be happy to be there with my PhD supervisor, close friends and fellow promovendi.

Due to the pandemic, this celebration we postponed twice. But it will finally happen in may 18 at the Uppsala Castle, how fancy!

Promovendi ceremony. Main University building
Banquet at Uppsala Castle
More banquet at Uppsala Castle

The event is so important that also canons are fired several times during the day to celebrate the importance of PhDs!

And here’s more info: https://www.uu.se/om-uu/akademiska-traditioner/promotion/

Annotating video and sound with Blender

What is Blender

People who know me know I love Blender. Some people don’t know what is Blender though. It was conceived first as a 3D modelling and animation tool but you can do a lot of things with it, such as video editing (which includes sound).

Video editing
Animation
3D and 2D modelling

Blender runs in all OS, Linux, Mac, Windows. you can download it here.

Annotating

If you have video or sound to annotate, although Blender is a very powerful tool, it’s maybe overwhelming at first sight. So I will show you in few easy steps how to annotate and export annotations.

In case you didn’t know, video and sound have frequencies and speeds. Things like 24 frames per second or 24000Hz, think about this when you edit or annotate video.

First open blender and select video edition, either in File > new > video editing. Or in the splash screen

Once you see the main workflow window for video editing simply drag your video or your sound into Blender, or open it from the file explorer on the side. Video is the blue channel, sound is green.

Annotations can be added with text effect strips. You can modify the text in the right hand menu.

If for some reason the menu is not there, hover over the sequencer section and press "N".

If your sequencer view is too narrow, zoom in with the mouse wheel. You can drag the darker sides of the annotation or move it around to make it as long as you need.

Remember to save continuously with ctrl+s or in file > save.

Export annotations

Blender has a built in text editor and code console. It uses python and has a python API called BPY. You can open a console in any location within Blender. Let me tell you how.

Blender can have many sub windows in which you can customize your workflow, such as in the first images I showed you. You can create any number of such windows by dragging any top right corner of a subwindow.

Open a text window, create a new text and add this code:

import bpy

f = open('filetosave.txt', 'w')

fstarts=[]
texts=[]

for i in bpy.data.scenes["Scene"].sequence_editor.sequences_all:
    if type(i) is bpy.types.TextSequence:
        print(i.text)
        texts.append(i.text)
        fstarts.append(i.frame_start)

fstarts, texts = zip(*sorted(zip(fstarts, texts)))

for i in zip(fstarts,texts):
    print(i)
    f.write(f'{i[0]}:{i[1]}\n")
        
f.close()

And this way you can export to a txt, all your annotations and the frame in which they occur.

But the frame is not the time. so you can modify to code to print the time instead by dividing by the fps of your video. If your fps is 24, then 240 frames are 10 seconds.

You can see your fps here:

Blender API

You can see in the code the kind of things you can get from your text strips, see more here: https://docs.blender.org/api/current/bpy.types.Sequence.html#bpy.types.Sequence

In this case, everything, video, sound, image, effect, is a sequence.

Annotating with images

You can add anything you want in the sequencer, images, sound and more video. Just drag it in move it around, expand it to cover the area you like and voilà. Use the menus to the right to modify aspects about this image like size, shape rotation location within the video.

Johan’s defense

My beloved Johan Öfverstedt is defending his thesis on February 25th, 2022. At 13:00 in Uppsala University, Sweden (see other world times here). Here’s some handy info for those interested in the event, I also wanted to summarize it in this post.

Location

New Ångström. Heinz-Otto Kreiss lecture hall, first floor

Opponent and committee

Opponent:

Prof Mattias Heinrich
Universität zu Lübeck

Committee:

Marleen de Bruijne
Antonella Zanna Munthe-Kaas
Fredrik Kahl
Joel Kullberg

Thesis document

The published thesis is available for free in the University Library, take a look and share it!

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 general zoom presentation:

https://uu-se.zoom.us/j/61355566195


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

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