CATMAID

A Collaborative Annotation Toolkit for Massive Amounts of Image Data

[Zlatic Lab @ZlaticLab]

👋 It is out! Our joint effort to create a complete synaptic connectome of Drosophila larval brain came true and is published in @ScienceMagazine: https://t.co/OCjqSSsReJ
Amazing work by @WindingMichael, @bpedigod + colleagues from @MRC_LMB @Cambridge_Uni @HopkinsEngineer @JHUBME

[Michael Winding @WindingMichael]

We’ve generated a synapse-resolution map of an insect brain, includes 3016 neurons and half a million synaptic sites! Out today in Science https://t.co/l3W5PEbhtJ

Summary below and in @bpedigod’s thread. @ZlaticLab, @albertcardona, @neuro_data, Carey Priebe, and many others

[Michael Winding @WindingMichael]

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 https://t.co/DfzqHxhdVk

[Tom Kazimiers @tomkazimiers]

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: https://t.co/sydSGFdSv9 There are many other great talks as well! #PostGIS #PostgreSQL

[Tom Kazimiers @tomkazimiers]

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

[CATMAID @catmaid]

Congratulations, fantastic work!

[CATMAID @catmaid]

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

[Current Biology @CurrentBiology]

Out now! Triple whammy of #Drosophila #connectomics 1 hygro-and thermosensory systems by @gsxej & colleagues https://t.co/N6OdnELwzu

[Greg Jefferis @gsxej]

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 https://t.co/7MjpApw4rB

[Tom Kazimiers @tomkazimiers]

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.

[Tom Kazimiers @tomkazimiers]

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.

[Andrew S. Champion @[email protected] @aschampion]

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

[Andrew S. Champion @[email protected] @aschampion]

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

[Tom Kazimiers @tomkazimiers]

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.!

[Florian Jug @florianjug]

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 https://t.co/LDFIHApAPG

[CATMAID @catmaid]

And this is the recording of the CATMAID release 2018.07.19 demo talk with @tomkazimiers: https://t.co/nKSqCOEzxX

[CATMAID @catmaid]

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.

https://t.co/Ta04AMdXgX

[HHMI | Janelia @HHMIJanelia]

Janelia scientists have imaged a complete adult fruit fly brain at nanoscale resolution, offering a new tool for researchers and uncovering new surprises. https://t.co/IUszYLylrN

[Greg Jefferis @gsxej]

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.

[Davi Bock @dddavi]

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