A Collaborative Annotation Toolkit for Massive Amounts of Image Data
Joined March 2016
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CATMAID retweeted
👋 It is out! Our joint effort to create a complete synaptic connectome of Drosophila larval brain came true and is published in @ScienceMagazine: science.org/doi/10.1126/scie…
Amazing work by @WindingMichael, @bpedigod + colleagues from @MRC_LMB @Cambridge_Uni @HopkinsEngineer @JHUBME
CATMAID retweeted
We’ve generated a synapse-resolution map of an insect brain, includes 3016 neurons and half a million synaptic sites! Out today in Science science.org/doi/10.1126/scie…
Summary below and in @bpedigod’s thread. @ZlaticLab, @albertcardona, @neuro_data, Carey Priebe, and many others
CATMAID retweeted
Check out our new preprint: the complete #connectome of the entire #Drosophila larval brain, with all inputs and all outputs, and a comprehensive analysis of feedforward and feedback pathways across both brain hemispheres #Neuroscience biorxiv.org/content/10.1101/…
CATMAID retweeted
Tomorrow is #PostGISDay 2021 and I am going to give a short talk on how and why @catmaid uses @postgis to query parts of brains in 3D space. "Neuroscience in the database" starts at 15:00 CET: info.crunchydata.com/en/post… There are many other great talks as well! #PostGIS #PostgreSQL
CATMAID retweeted
After spending some time dabbling in Rust and WASM over the holidays, @catmaid now finally supports simple Neuroglancer precomputed datasets directly. Thanks to @aschampion's n5-wasm and rust-n5 libs and image block layer, there are now first versions of ngpre-wasm and rust-ngpre
Congratulations on these new publications---an amazing collaborative effort! Including many nice reconstructions of neurons and their connectivity, created in the FAFB CATMAID instance (manual + segmentation). Soon to be shared through @virtualflybrain. #drosophila #connectomics
Out now! Triple whammy of #Drosophila #connectomics 1 hygro-and thermosensory systems by @gsxej & colleagues cell.com/current-biology/ful…
CATMAID retweeted
Excited to share our @biorxivpreprint: #connectomics reconstruction of olfactory circuits in the #Drosophila brain led by @as_bates @MRC_LMB, @uni_matrix @martamcosta2 @CamZoology. Collaboration with @ddavi, @ScottishWaddell, Gerry Rubin @HHMIJanelia 1/12 biorxiv.org/content/10.1101/…
CATMAID retweeted
Beautiful! And a big collaborative effort in a single @catmaid setup with ~275 users who created ~44MM nodes that make up ~1.2MM neurons + fragments (= ~10.7m!), connected through currently ~1.1MM synaptic nodes. All software open source, relying on @PostgreSQL + @djangoproject.
And check out the stunning front cover made by @uni_matrix using the current tracing in the @dddavi FAFB volume
CATMAID retweeted
Thanks to comments by Jürgen Rybak and Lydia Gruber at @MPI_CE I added simple absolute polyadic synapse coloring to @catmaid. It color-codes the number of postysynapses and sometimes reveals small patterns, like in these Drosophila larva L1 Kenyon Cells traced by @EichlerKathi.
ALT More postsynapses for presynapses in the left part of the image of these Kenyon Cells.
CATMAID retweeted
Ever wanted to stand inside a mushroom body? Thanks to @CATMAID, #webvr (via Firefox @mozillareality), and a snow day at Janelia this week that left me cooped up with a Samsung Odyssey+, you can.
Drosophila larva connectome reconstruction courtesy @albertcardona @EichlerKathi
CATMAID retweeted
Projecting neurons reconstructed in ssTEM of one Drosophila larva into FIBSEM of another. Different animal, different microscopy, different orientation, same great @CATMAID taste. Enabled by awesome federation tools from @tomkazimiers
CATMAID retweeted
The next @catmaid release adds integrated NBLAST. It allows similarity ranking between neurons, landmark transformed neurons and point clouds (e.g. from LM data) to help find/match/identify neurons plus LM data. Thanks to @gsxej and others for the useful R nat.nblast ref. impl.!
ALT NBLAST support in CATMAID: construct similarity matrices, find similar neurons (top view) and point clouds (bottom view and right column), use landmarks to transform neurons (e.g. contralaterally) and use NBLAST with them (top view), visualize the results.
CATMAID retweeted
1 day left to register for #I2K
Teaser: Neuronal circuit mapping & analysis with @catmaid -- circuit graphs, Venn diagrams of synaptic partners, 3D morphology visualizations, arbor synapse distrib., etc.
This and more from my father, @albertcardona, at embl.de/training/events/2018…
New CATMAID release 2018.07.19 brings more volume intersection tools, 3D line width adj. on all platforms, better 3D catalog export, tracing data FOV constraints, more fine grained sampling options + more. Also it is the last version supporting Python 2.
github.com/catmaid/CATMAID/r…
And this is the recording of the CATMAID release 2018.07.19 demo talk with @tomkazimiers: youtu.be/ikRlZBI0BTo
CATMAID retweeted
Janelia scientists have imaged a complete adult fruit fly brain at nanoscale resolution, offering a new tool for researchers and uncovering new surprises. bit.ly/2Nt1i3K
CATMAID retweeted
As @zhihaozheng points out in response below, you absolutely can explore this awesome whole fly brain EM dataset from @dddavi and crew online in CATMAID thanks to work of @virtualflybrain (shout out to Rob Court @EdinburghUni) & image data hosted in Cambridge @MRC_LMB.
This is a monumental achievement. But why cannot we EXPLORE the data? No one wants to download 12 TB of image data. Particularly not when everything is available through @catmaid that was designed specifically to make such massive datasets easily accessible to everyone!
CATMAID retweeted
And, a preview of what the whole fly brain EM dataset's user community has been up to while we rewrote, etc. ~5 mm traced cable length shown here!
beautiful visualization by @uni_matrix, somewhat mangled by my downsizing & trimming to only 180° rotation
#ASAPbio #bioRxiv