a little bit of everything

Category: Machine Learning

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 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

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