Ana Marija Jakšić
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merianelion.bsky.social
Ana Marija Jakšić
@merianelion.bsky.social
1.4K followers 3.4K following 140 posts
Group leader @ Jaksic Lab, EPFL, ELISIR scholar, Drosophila, Neuroscience, Topology, Robots, Evolution, PopGen, Cognition, Corals, she/her, Trekkie utopian 🦄🧬🪰🧠🪸🇪🇺🇨🇭🇭🇷 🌍🖖🏻 On the faculty job market
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merianelion.bsky.social
Mouse brain, the next TopoTome step towards the holy grail
October 6, 2025 at 9:06 PM
merianelion.bsky.social
🚨Preprint🚨
What started as an attempt to compare CT scans of diverse fly brains, ended up a new concept for analysis & segmentation of difficult tomographic data. No ground truths, no training, just maths. This is TopoTome, topological data analysis of 3D images

www.biorxiv.org/content/10.1...
Figure showing 3 panels. Panel A: workflow of a classical deep learning model vs TopoTome workflow, with marked differences between the methods, including manual segmentation of images, design and optimization of neural network and data post processing that is needed in deep learning workflow but not in TopoTome. Panel B: core concepts behind TopoTome shown connected by arrows. From left to right, there is a microCT scan of a fly brain (3D reconstruction), a persistence barcode of H2 homologies, an image of how persistent barcodes map to the original CT brain scan, and a segmentation of a CT scan. Panel C shows the concept of cubical complex filtration of 2D and 3D image data.
September 30, 2025 at 9:58 AM
merianelion.bsky.social
My lab cannot afford donating at the moment, so I donated privately. Even if you don’t work on flies we all owe so much to FlyBase. Consider donating, and importantly, let’s strive to make the more official funding bodies aware of how much is at stake.
August 27, 2025 at 8:07 AM
merianelion.bsky.social
There are now three printed PhD theses on my bookshelf 🥹
Books on bookshelf. Two champagne corks jn front of them. Book titles from left to right: The Mind of a Bee, Time Love Memory, Osnove Genetike, Ecological Genetics and Evolution, PhD thesis by AM Jaksic, PhD thesis by Riddha Manna, PhD thesis by Samuel Bourgeat, On the origin of species, Imaginary animals, Historija filozofije, Population genetics, Progress and prospects in evolutionary biology: the Drosophila model.
July 4, 2025 at 3:11 PM
merianelion.bsky.social
Why is academia riddled with stale, incremental “low hanging fruit” science programs?

When we make decisions on what kind of science to pursue, we can optimize for career payoff or scientific payoff, almost never both.

I know I’ll always pick exciting science despite the cost.

How about you?
Screenshot of text: Of course, scientists' actions, especially their effort, are observable to those around them - their bosses, their colleagues, their family, and their friends. But these are not the people who ultimately determine whether scientists get the university tenure-track job or are honored by a professional society. Instead, career success accrues based on how the scientific community evaluates scientists' contributions. Thus, it is the scientific community that serves as the ultimate arbiter of investigators' professional success, and this community does not have the means (because of its physical dispersion) or perhaps even the interest to monitor investigators' effort. Indeed, to a first approximation, scientists' careers rise and fall based on their CVs, and CVs list only scholarly outputs, not hours worked or risky undertakings gone bust. Screenshot of text: In deciding how to reward discoveries, the scientific community must contend with the fact that reward schemes that motivate effort inherently discourage scientific risk-taking and vice versa. Because the community must motivate both effort and scientific risk-taking, and because effort is costly to investigators, the community inevitably establishes a tradition that encourages more conservative science than would be optimal for maximizing scientific progress, even when risky research is no more onerous than safer lines of inquiry.
July 2, 2025 at 7:51 AM
merianelion.bsky.social
Bumped into this meme on reddit and omg it’s so true and hilarious that I just had to make a real photo version of it 😂
May 30, 2025 at 2:23 PM
merianelion.bsky.social
I had a magical time at the University of Oxford - I stayed at a Magdalen College cloister, strolled through the School of Divinity, gave a talk and spent an amazing science day visiting the DPAG. Thanks to Scott Waddell for hosting me!
Still in awe of the Oxford vibe, I hope to return there soon 🧙
May 29, 2025 at 10:15 AM
merianelion.bsky.social
Another huge day for Jaksic lab!
I’m so profoundly proud of Samuel Bourgeat, the second PhD student from the lab defending his thesis today! It was a true privilege to see him grow into a scientist he is today and can’t wait to see the amazing science he will do in the future!

#proudPI 🧠🪰🧬🧪
May 22, 2025 at 4:27 PM
merianelion.bsky.social
The fact that a university like Harvard has an endowment larger than the complete budget (not science budget, but like the whole state budget) of my European home country makes the whole situation even more ridiculous.
Meme, showing in upper panel an adult woman holding a gleeful child in a pool. Nect to them another child is struggling to swim, almost drowning with no support. In bottom panel a skeleton sits in a chair at the bottom of the sea. Text next to adult woman sYs “ERC funding”, next to the gleeful child “US scientists”, next to drowning child “European scientists”, next to the skeleton “Eastern European scientists”.
May 17, 2025 at 11:27 AM
merianelion.bsky.social
I’ve just spent a few days in Barcelona and the ALBA #synchrotron, where I’ve been imaging, studying and admiring complex structures of many sorts. I haven’t been this excited about a project in a very very long time! 🤩 🧠 🪰🔬🧪 #neuroskyence
Selfie of a woman with glasses in front of sagrada familia basilica in Barcelona Selfie of a woman with glasses in rainbow-colored sweater in front of a complex machine in the synchrotron facility Selfie of a woman with glasses in front of a complex machine in the synchrotron facility
May 15, 2025 at 1:33 PM
merianelion.bsky.social
We’ve pushed our CT to its very limit, and perfected the staining. We’re already deep in the nano scale, and so so ready for the synchrotron. Next step, the connectomeS! 🧠🧪
May 9, 2025 at 2:43 PM
merianelion.bsky.social
Gmail slaying with the suggested reply buttons, I’m tempted to hit the second one 😂
Reply buttons suggestion in gmail inbox: 1. “Thank you for your reply.” 2. “Bummer!” 3. “Thanks for trying!”
May 2, 2025 at 6:21 AM
merianelion.bsky.social
We’re one step closer to the grand goal every day, but this step was particularly fantastic :)
May 2, 2025 at 5:43 AM
merianelion.bsky.social
I’m on a train back home from Freiburg, where I spent a wonderful day with the people from the Max Planck Institute @mpi-ie.bsky.social and Iovino lab. All around very cool science and wonderful people! And to end this trip on a most lovely note - a surprise breakfast birthday cake from the hotel 🥰
March 28, 2025 at 8:31 AM
merianelion.bsky.social
All neurons are beautiful but there are some that are also stunning
Image of a very branched-out purple neuron on a white background
February 17, 2025 at 1:36 PM
merianelion.bsky.social
25th Swiss Society for Neuroscience meeting has come to an end! I had a great time being a part of the local organizing committee and I’m very happy with the interest my fellow neuroscientist have shown for our non-mammalian fundamental neuroscience model systems!
CT scan of a bumblebee brain
February 7, 2025 at 7:36 PM
merianelion.bsky.social
Not often do I fly in such good company 🐜
A transparent box containing ants, pictured in front of a plane seat A close-up of the ant colony in a box
December 20, 2024 at 10:09 AM
merianelion.bsky.social
A wonderful time at Johannes Gutenberg University in Mainz has come to an end.
Thank you to everyone I met today for a great day filled with inspiring science and discussions, especially Carlotta Martelli and Marion Sillies for the invitation and hosting
The Mainz cathedral dome is visible behind Christmas market decorated with christmas lights and filled with people. It is nighttime.
December 19, 2024 at 11:16 PM
merianelion.bsky.social
First PhD of the lab is now offical!
All went well, except I almost forgot to hand over the diploma at the end 😅 I chalk it up as an emotional fumble 😇Congratulations Dr. Manna!
@riddhamanna.bsky.social
Riddha Manna & Ana Marija Jaksic smiling, Ana with a thumb up and Riddha holding a red doctorate diploma
December 17, 2024 at 5:24 PM
merianelion.bsky.social
Overleaf being down today finally gave me some time to beautify these two forceps abominations 🫠
Images 1,2: Before
Images 3,4: After
Close-up of the tip of superfine metal forceps as seen through a binocular. Tips are bent, broken and dirty Close-up of the tip of superfine metal forceps as seen through a binocular. Tips are bent and do not align at the very end Close-up of the tip of superfine metal forceps as seen through a binocular. Tips are shiny and well aligned Close-up of the tip of superfine metal forceps as seen through a binocular. Tips are shiny and well aligned
December 3, 2024 at 3:40 PM
merianelion.bsky.social
A huge day for my lab - the first PhD student, Riddha Manna, successfully defended his thesis today! 🥳🎊🎉🍾🥂
Riddha Manna and Ana Marija Jaksic, smiling and together holding a printed out PhD thesis. A champagne cork on a desk with a writing on it saying “Riddha Manna 02.12.2024” Riddha Manna, Anne-Florence Bitbol, Richard Benton, Kathryn Hess and Ana Marija Jaksic, standing in front of a screen projecting two zoom windows. In zoom there is Johannes Felsenberg with his thumb up, and Michale Herzog.
December 2, 2024 at 7:54 PM
merianelion.bsky.social
Feels nice to see the 1st citation from my lab’s experimental paper cited alongside the opinion piece by Kandel from 1992 😎
Now that we know what it took to do this experiment, it’s no wonder nobody was crazy enough to try it for the past 30 years 😅
Screenshot of a paragraph saying “The assumption of individuality in learning is supported by a body of knowledge from both neurobiolog and theories of learning and instruction. Neurobiology emphasizes how genetic makeup and personal history interact to shape individual behavior through learning processes, which modify the brain's structure in slightly different ways for each of us, thereby creating the biological basis for interpersonal differences (Kandel & Hawkins, 1992; Manna et al., 2024).” Sentence starting with “Neurobiology emphasizes…” is highlighted
November 25, 2024 at 2:42 PM
merianelion.bsky.social
The only thing that makes me not melt down (like my 3D printer’s print head) about lab equipment failure is the fact that it usually provides me with a hands-on problem with a clear goal and solution - so rare when you’re a PI. Spent a very satisfying morning fixing and recalibrating the 3D printer
Inside of a 3D printer with a badly clogged print head. Printing filament is overflowing the print head and dripped and melted on the print bed. Faild print part detached from the print bed and is stuck under it Newly installed print head as seen from the top, printing out a XY axis calibration grid with two different types of filaments A properly printed Benchy model still attached on the print bed. Benchy is a small model of a boat, used for troubleshooting 3D print quality.
November 22, 2024 at 11:58 AM
merianelion.bsky.social
Please add me and my academic colleague Schaffica :)
A dog, white standard poodle, sitting in a chair in front of a laptop and a coffee cup. A dog, white standard poodle, extending her front leg and paw towards the camera to hold a human’s hand. There’s an aquarium & a yellow sofa in the background.
November 18, 2024 at 12:46 PM