4/ Heavily inspired from TNIA (Brian Northan @truenorth-ia.bsky.social) & stackview (Robert Haase @haesleinhuepf.bsky.social), and of course the marimo team / anywidgets! If missing similar tools, feel free to add them below. Hope you find the tool useful - lmk if you have thoughts / feedback!
3/ Try it here on google colab: colab.research.google.com/github/eigen... (remember to press ‘C’ to Center the view on mouse hover), or in molab / marimo.app @marimo.io (edit) molab.marimo.io/notebooks/nb...
2/ Inline, interactive 3d ortho-viewer (multichannel), with position/projection thickness, brightness-contrast, point annotations, and more! Because it is written in `anywidget` and `matplotlib`, this viewer will run on your preferred notebook environment (colab, jupyter, marimo)
1/ 🔬🧑💻 Tired of going back and forth between GUIs and code for your 3D image analysis needs? Would you like to keep your focus in one place (notebook), without sacrificing interactivity? Here’s a tool that can help!
Yep, it lags a little. But still quite impressive considering that each "pixel" is a 150 MPixel multires image. Overall the total number of 'adressable' pixels in this 2D image are 225x225x150 Mpix = 7.6 Tera pixels. #ImageJ #Fiji #BigDataViewer
Quote card from author Nandan Nerurkar, Columbia University, USA. "Open Access is the right thing for science, and it's so much easier to do the right thing when it's free! I'm grateful to The Company of Biologists and Columbia University for absorbing the cost of open access publishing through Read & Publish agreement. This will expand the reach and accessibility of this exciting work by postdoc Lisa Calvary and PhD student Panos Oikonomou from the lab."
Thank you, Nandan Nerurkar, for sharing your experience of fee-free #OA publishing in @dev-journal.bsky.social via our #ReadAndPublish agreement with @columbiauniversity.bsky.social @nerurkar.bsky.social.
Read Nandan’s paper: bit.ly/4pkw7Jh
1/ 🐣⚒️ To study mechanics, we need to apply prescribed forces - how can we do that in living tissues? I am @eigenp.bsky.social and in this thread I'll highlight our new approach for applying tension on epithelial tissues in vivo!
New preprint from my PhD in @amphispacelab.bsky.social is out! 🥳
We investigated the evolution of my favorite gene FoxQ2 across 21 animal phyla, and found three ancient paralogs with a very dynamic history.
More on phylogeny, synteny, and comparative in situs in the 🧵 below!
tinyurl.com/2j96px45
#MicroscopyMonday 🔬 MBL Research Scientist @ryliewalsh.bsky.social imaged this chick embryo, labeled with DAPI (a DNA stain) and fibronectin (a glycoprotein), on the MBL's stage-scanning line confocal microscope.
Specimen courtesy Panos Oikonomou, Columbia Univ.
www.youtube.com/watch?v=jAUo...
For my first post on 🦋, I am incredibly excited to share that my PhD paper has been published in #ScienceAdvances!
We compared the development of the anterior neuroectoderm to uncover how the chordate #forebrain evolved 🧠. Have a look at the summary 🧵 below!
www.science.org/doi/10.1126/...
