Rafael Camacho Podcast
By Rafael Camacho
Rafael Camacho PodcastJan 17, 2022
#8 Jean-Yves Tinevez: Tracking objects in biological imaging, a history of experimental physics, microscopy, and software.
My guest on this occasion is Jean-Yves Tinevez, research engineer and head of the image analysis hub at the Institut Pasteur.
I have the great privilege of now considering Jean-Yves a friend. However, some years ago, I was just a fan of his work, particularly trackmate. His reaction to me letting him know of this small piece of history was a true testament to his character. Jean-Yves is brilliant, loves the community he is part of, and conducts himself with great humility, he even reveals in our conversation some of the ways in which he checks his ego, making sure it does not grow more than he sees fit.
We go over many topics, discussing his love for experimental physics, how the need for better measurements and his personal skill sets drove him to develop trackmate, and how trackmate and other software he developed and maintains have evolved to tools used by the bio-image analysis community at large.
I hope that you find this conversation as interesting as I did.
Links for the episode:
Jean-Yves at Pasteur: https://research.pasteur.fr/en/member/jean-yves-tinevez/
Twitter account: @jytinevez
Github: https://github.com/tinevez
Trackmate: https://imagej.net/plugins/trackmate/
ESP1 - FIJI e inteligencia artificial para el análisis de imágenes biológicas
Para este podcast he tenido el privilegio de conversar con Ignacio Arganda-Carreras. Ignacio es un investigador en el área de inteligencia artificial con aplicaciones a bio-imagen. Ignacio trabaja en la Universidad del Pais Vasco para el Departamento de Ciencias de la Computación e Inteligencia Artificial de la Facultad de Informática. Si son usuarios de ImageJ o FIJI, entonces el nombre de Ignacio esta asociado con distintos plugins muy populares, entre ellos, dos de mis favoritos: Trainable Weka Segmentation, y MorphoLibJ.
En esta oportunidad Ignacio y yo hablamos acerca de sus inicios en ImageJ, como desarrolló plugins que le eran útiles y finalmente a se involucro mas de lleno en el grupo de desarrolladores de FIJI. También hemos hablado un sobre inteligencia artificial y cómo estas técnicas han entrado en el ámbito de la bioImagen.
En lo personal este podcast fue muy especial ya que es el primer audio que publico en español y no pude tener mejor compañía que la de Ignacio. De nuevo Ignacio muchas gracias por aceptar mi invitación y por nuestra charla tan amena.
Links para el episodio:
Página web de Ignacio: https://sites.google.com/site/iargandacarreras/
Twitter: @IgnacioArganda
ImageJ, people: https://imagej.net/people/iarganda
FIJI: https://imagej.net/software/fiji/
Trainable Weka Segmentation: https://imagej.net/plugins/tws/
MorphoLibJ: https://imagej.net/plugins/morpholibj
Irkebasque: https://www.ikerbasque.net/ignacio-arganda-carreras
#7 Johanna Bischof - Scientific project management at Euro-BioImaging
For this podcast, I had the great pleasure of speaking to Johanna Bischof.
Johanna works as a Scientific Project manager at Euro Bioimaging. Euro-Bioimaging is a research infrastructure that offers access to imaging technologies in biological and biomedical imaging.
Johanna and I met each other some time ago and one of the most obvious things about her is that she loves microscopy, talking to people, and science communication. So I guess you can tell why she was an obvious choice as a guest for the podcast.
In our conversation, we discuss how she discovered fluorescence microscopy, her background as a scientist, and her transition to Scientific Project manager at Euro-Bioimaging. I had a lot of fun talking to Johanna and I hope you also enjoy our conversation.
Johanna's Twitter account: https://twitter.com/JojoBischof
Euro BioImaging: https://www.eurobioimaging.eu/
Euro BioImaging virtual pub: https://www.eurobioimaging.eu/about-us/virtual-pub
#6 Sebastian Rhode - Microscopes and Image Analysis in Industry and Academia
My guest in this podcast is Sebastian Rhode, Senior Product Owner in Machine Learning and Image Analysis at ZEISS microscopy (https://www.zeiss.com/microscopy/int/home.html).
If you are involved in bio-image analysis, NEUBIAS or the imge.sc forum then you probably know Sebastian. He is extremely active in the community, not only showing what ZEISS can do in this arena but also interacting and helping the open-source community when they have questions regarding ZEISS image format or their products. (https://github.com/zeiss-microscopy/OAD)
For me, this podcast was a unique opportunity to chat about the interaction between academia and industry, and between the open-source community and the commercial solutions. We also cover many other topics, such as football, the love of building microscopes, smart microscopy, teaching, trust, hardware vs software, academia vs small and large companies and much more.
I had a blast talking to Sebastian and I am sure we could have kept talking many hours more, thus I am sure that if time allows we will have many more conversations in and off the podcast record.
Sebastian's Twitter account: https://twitter.com/sebisabs
Time stamps for the episode
(00:00) Introduction
(01:33) Football
(06:00) Laser safety and dye lasers
(09:25) Lasers vs objectives who wins?
(12:05) Chemistry, spectroscopy and microscopy - the love of building microscopes
(15:40) Physics and Russians
(19:40) Sebastian in academia
(22:12) Transition from academia to industry
(25:30) Starting in industry
(28:50) Changes and surprises when moving to industry
(34:00) Interaction between academia and industry
(37:00) Moving to a different and larger company
(40:00) Job security
(45:00) Communicating and hiring in industry
(50:50) Sebastian goes to ZEISS
(55:30) Metal and glass vs software
(1:06:00) Developing software for microscopes
(1:09:30) BioImage analysis and NEUBIAS
(1:11:30) Industry engaging with open software communities
(1:15:30) The price of software
(1:21:20) Image analysis for industry vs life science research
(1:29:34) First impressions count: simple vs flexible
(1:35:37) How to prove that a software tool generates value
(1:37:50) Closing remarks
#5 - Anna Klemm: Bioimage analysis, facilities, and the nordics
While Anna and I are in many ways colleagues, connected via bioimage analysis and Scilifelab, we don't share the workspace, and we usually don't get the chance to just talk. It was great to have her on the podcast and talk about her transitions from researcher to facility staff, from Germany to Sweden, how did she get involved with NEUBIAS, women in science, etc.
I hope you enjoy listening to this as much as I did talking to Anna
Relevant links to some of the topics in the episode:
BioImage Informatics Facility, at SciLifeLab: www.scilifelab.se/facilities/bioimage-informatics/
Anna's Twitter account: twitter.com/ahklemm
Anna's GitHub account: github.com/ahklemm
Anna's webinar on ImageJ/Fiji Macro Language: youtu.be/o8tfkdcd3DA
Imagesc Forum: forum.image.sc/
NEUBIAS: eubias.org/NEUBIAS/
NEUBIAS youtube channel: www.youtube.com/channel/UC-oy7UpEhRfHQ-5ePCviKFg
Fabricio Jimenez - Particles and Music
Fabricio is a postdoc in the LLR laboratory at École Polytechnique of Université Paris-Saclay. Fabricio is an experimental particle physicist and a friend of mine for many years. This conversation was quite special to me as I haven't seen Fabricio in a while and we got to talk about many of the things we love, mainly physics and music. Fabricio is a brilliant guy and a very good amateur musician.
During the first 30 minutes of our chat, we concentrate on physics and his experience in the field of particle physics during the last 30 minutes we talk about music and Venezuela, our home country. He then closes the episode with a nice gift, a traditional song from our home. I hope you enjoy listening to this as much as we did talking to each other.
Useful links
Fabricio's Twitter account: @fabriciojm
LLR laboratory: https://cms25.web.cern.ch/institutes/LLR-France/
Interested in the Venezuelan cuatro: https://tucuatro.com and https://www.youtube.com/user/TuCuatroDigital
Jakob Blomquist - Part 2 - Martial arts: Aikido and his interplay with Jakob's life and science
Jakob is a lecturer at Malmo University and a 5th dan Aikido practitioner. In this episode, we concentrate on the topics of martial arts, particularly Aikido, and its interplay with his scientific career and life in general. We talk about Ukemi, the art of receiving or in other words handling an attack or technique, managing aggression, discipline and creativity, and how the current pandemic has affected our life, considering how important the Dojo is for our physical and psychological health.
Useful links
Jakob's website: https://jakobblomquist.wordpress.com/
Jakob's university site: https://mau.se/en/persons/jakob.blomqvist/
Jakob's Twitter: https://twitter.com/BlomquistJakob
Jakob's Instagram: https://www.instagram.com/jakob_blomquist_aikido/?hl=en
Lund's Aikido club: https://www.lundsaikido.se/english/
Jakob Blomquist - Part 1 - Science: Surface chemistry and his path through science
Jakob is a lecturer at Malmo University and a 5th dan Aikido practitioner. In this episode, we concentrate on his path through science, and his work is surface chemistry, DFT calculations, and the chemistry of water. Although Jakob and I know each other for many years I have never heard in detail about this part of his life, so I tended to listen and enjoy, I hope you enjoy it too.
Useful links
Jakob's website: https://jakobblomquist.wordpress.com/
Jakob's university site: https://mau.se/en/persons/jakob.blomqvist/
Jakob's Twitter: https://twitter.com/BlomquistJakob
Jakob's Instagram: https://www.instagram.com/jakob_blomquist_aikido/?hl=en
Lund's Aikido club: https://www.lundsaikido.se/english/
Robert Haase - Bioimage analysis, smart microscopy, GPU acceleration and open-software development
Robert Haase is a group leader and bio-image analyst at the DFG Cluster of Excellence "Physics of Life" TU Dresden. In this conversation Robert and I go over many interesting topics, covering the typical suspects (image analysis, software development, GPU acceleration) as well as some other technical and not so technical topics.
Relevant links to some of the topics in the episode:
Robert's group: https://physics-of-life.tu-dresden.de/en/research/technology-development-groups/bio-image-analysis
Robert's Twitter account: https://twitter.com/haesleinhuepf
Robert's GitHub account: https://github.com/haesleinhuepf
Robert's YouTube channel: https://www.youtube.com/channel/UC-hlwQ9Q4GS3rtv2EwSStAQ
CLIJ: https://clij.github.io/
clEsperanto: https://clesperanto.github.io/
Imagesc Forum: https://forum.image.sc/
NEUBIAS: https://eubias.org/NEUBIAS/
NEUBIAS youtube channel: https://www.youtube.com/channel/UC-oy7UpEhRfHQ-5ePCviKFg
Rubber duck debugging: https://en.wikipedia.org/wiki/Rubber_duck_debugging
Napari: https://napari.org/
ImageJ: https://imagej.nih.gov/ij/index.html
Biaflows: https://biaflows.neubias.org/#/
List of topics covered (in order or appearance, sort of):
Beers - Holsten dreht am dollsten.
Robert's new role as principal investigator/group leader
Robert's history as a software engineer
Bio-image analysis
Beatles and smart microscopy
Light-sheet microscopy
GPU acceleration
Big-data
Bugs and software development
Fear of programming
Teaching and remote teaching
NEUBIAS
Naming conventions in bio-image analysis
Rubber duck debugging
clEsperanto
Building bridges between developers, analysts, and biologists
ImageJ / FIJI
Napari
Developers and users interaction
Sustainable software development
Biaflows
Robert's retirement plan
Open-source
Docker technology
Weather in the north
Remote collaboration