a little bit of everything

Month: April 2021

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 Ă–fverstedt.
  • 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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