New collaborative paper

Very happy to see the publication of the manuscript describing “PlantSeg” a tool for the accurate and versatile segmentation of plant tissues into cells.

It has been a great team work together with Adrian Wolny & Lorenzo Cerrone from the labs of A. Kreshuk & F. Hamprecht (EMBL & Uni Heidelberg) as well as Kay Schneitz’s lab (Athul Vijayan, Rachele Tofanelli – TU Munich) and many others.

PlantSeg uses neural networks and diverse segmentation algorithm to segment plant cells in 3D in complex tissues. You can feed it confocal or light sheet images. We showcase its performances on lateral roots, ovules, shoot meristems, leaves and many more tissues. It works so well, that it can even segment non plant images (e.g. fly wing disc).

See: https://elifesciences.org/articles/57613 and https://github.com/hci-unihd/plant-seg

Resources for online teaching

The Covid-19 outbreak has catalysed the need to be able to teach online. Yet, reinventing oneself in a professional YouTuber is not something done in one night. Heidelberg university has made a lot of tools and some resources available for online teaching on a short time, this was a great starting point. However most to all of these helps where in German and did not cover all needs.

While experimenting how I would move my lectures to asynchronous online lectures, I have tested several solutions and created a series of video tutorials in English that cover:

  • Part 1: How to create recordings of lectures using open source, free, cross-plateform software OBS
  • Part 2: How to edit
  • Part 3: How to compress
  • Part 4: How to upload/share them via Moodle

These videos and the ones to come are available on the lab Youtube channel:

Feel free to distribute these links.

Adapting to Corona times

As everyone else since several weeks, the lab has to adapt to the COVID-19 outbreak. Here is a short summary of how it went/goes for us and we handled / are handling it.

It all started mid-March with 2 weeks of reduced activity, during which we finished running experiments, did not start any new ones and prepared for a looming lockdown. We reduced presence time in the lab to the necessary wet bench activities and shifted the computer work to home office and organized.

Then the lockdown of the University came and we were sent home until 20.04. During that time, we took turn to visit the lab three times a week to take care of the plants and check on the lab. We fully moved to computer work and each of us had specific tasks:

  • Michael, Jazmin and Zhaoxue: worked on drafting or fully writing manuscripts on their current projects.
  • Béatrice worked on writing her PhD thesis
  • Alexis worked on manuscript & grant reviews, writing manuscripts and spent hours   « Zoomed in » with colleagues to get the institute and teaching organised.

We kept weekly lab meeting, experimenting with different plateformes (Zoom, Webex, heiCONF…). We each reported on the work done, cross commenting on our drafts of figures and outlines and laid out our plans for the coming week. We had journal club too. Slack our beloved lab IM has been great at keeping us together.

I am very happy and proud of how the lab adapted, kept a good morale and worked during these weeks. We all had challenges to face: small apartments, flaky internet, children & homeschooling, but we kept the ‘ears stiff ‘ as the German saying go. Despite all this, great things were achieved and this time forced us to take more time to read, think and plan.

Now, work in the lab has officially resumed, but under strict distanciations rules to minimize the risk of spreading the infection while in the lab. Concretely, all office/computer work remains done at home, meetings and discussions online, and presence at the bench must be planned to minimise encounters. This is a bit of organisation challenge, but very much facilitated by the excellent join work with our neighbors labs (and Slack 🙂 ).

So right now we are slowly ramping up again, but challenges remain: we can’t host any students for the time being; we have trainees waiting to start but are keeping them on hold. This is however not sustainable for several months. Same for the rest of our activities, we are actively thinking about a work organisation that mitigate safety and efficiency and that we can maintain for the coming 6-9 months (it will take long to go back to any « normality »).

New paper: plasticity of early lateral root growth

Some early light sheet data of former co-supervised PhD student Daniel von Wangenheim and Jens Boland (Fengerau) have made their way in his last opus in the Bennett lab Nottingham. Daniel shows that that the radial positioning of emerging lateral roots is influenced by their hydrological environment (hydropatterning) and this starts during early developmental stages. You can read about it here: https://www.nature.com/articles/s41477-019-0580-z

Lab outing 2019

No aquatic adventure this year, December in Heidelberg is a bit too cold for it. Most people go to the Christmas Market, but the lab like to think different, so we took some “altitude” and went bouldering (after the annual lab cleaning):

the lab hanging in there… with (from back to front): Béatrice (climbing ninja), Amaya, Michael, Jazmin, Tuğçe, Mayra and Alexis

and concluded this exhausting session with delicious Thai food

now with Zhaoxue