Rafael Camacho Podcast Rafael Camacho

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/

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

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

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

Anna Klemm is the Head of the BioImage Informatics Facility, at SciLifeLab, in Sweden. SciLifeLab is a research infrastructure that provides access to a broad range of technologies in biosciences. Facilities like the one from Anna support scientists from academia, industry and health care. 
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: https://www.scilifelab.se/facilities/bioimage-informatics/
Anna's Twitter account: https://twitter.com/ahklemm
Anna's GitHub account: https://github.com/ahklemm
Anna's webinar on ImageJ/Fiji Macro Language: https://youtu.be/o8tfkdcd3DA
Imagesc Forum: https://forum.image.sc/
NEUBIAS: https://eubias.org/NEUBIAS/
NEUBIAS youtube channel: https://www.youtube.com/channel/UC-oy7UpEhRfHQ-5ePCviKFg

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