Show threadTeixiOct 11, 2024

@uni_matrix @davi

ps: also includes nice paragraph on #TrakEM2 by @albertcardona et al. w/ remark on alignments errors auto correction.

As for #catmaid collaborative annotation & neuronal structures skeletons approach!

Show threadAlbert CardonaMar 4, 2024

@adredish @neuralreckoning @brembs @ScholarNexus

Likewise for #TrakEM2, #FijiSc and #catmaid software – except we did write papers for them.

Albert CardonaSep 29, 2023

A connectome of the optic lobe of the extremely tiny fairy wasp, Megaphragma sp.

"A complete reconstruction of the early visual system of an adult insect", by Chua et al. 2023 (Chklovskii & Polilov) https://www.sciencedirect.com/science/article/pii/S096098222301237X

Don't miss the supplemental figures.

"Compared with the honeybee and the fruit fly, Megaphragma exhibits the following miniaturization-related adaptations: a significant reduction in the number of ommatidia, absence of several cell types, reduced size, and denucleation of neurons. Interestingly, the reduction in lens diameter is less than that expected from the optimization of the optical resolution of the eye. This suggests that light sensitivity is a more important
consideration when lens diameter approaches the wavelength of light. The absence of wide-field (or non-columnar) lamina neurons in Megaphragma could be a consequence of the smaller number of ommatidia, their larger acceptance angle, and the lower resolving power of the eye."

Volume assembled with #FijiSc and #TrakEM2, and its neurons and synapses mapped with #CATMAID. Woohoo!

#neuroscience #connectomics #VolumeEM #vEM #insects #miniaturization

Show threadAlbert CardonaSep 13, 2023

@yoginho @tyrell_turing

Rodney Douglas has always had a poetic, trascendent touch. Was great working alongside him back in 2005 for a brief while, when developing the #TrakEM2 software in Zurich.

Show threadAlbert CardonaAug 19, 2023

@carrerassanahuja

#TrakEM2:
* https://syn.mrc-lmb.cam.ac.uk/acardona/INI-2008-2011/trakem2.html
* https://imagej.net/plugins/trakem2/

És un plugin gros de #FijiSc: https://fiji.sc/

Et poso una captura de pantalla d'un fotomontatge automàtic:

TrakEM2

ImageJ plugin for morphological data mining, segmentation, 3D modeling, image stitching, registration, editing and annotation.

Show threadAlbert CardonaAug 19, 2023
@carrerassanahuja També ho pots fer amb #TrakEM2 i #FijiSc — però és més tècnic. Igualment de codi obert.
Show threadAlbert CardonaDec 12, 2022

@dantracey @kristinmbranson @annikabarber @debivort @giorgiogilestro

Find the original basin-1 neurons at the #VirtualFlyBrain at "Tools - CATMAID - Hosted EM Data - Larval - Larva (ABD1.5)" which opens a #CATMAID server https://abd1.5.catmaid.virtualflybrain.org/?pid=1&zp=10485&yp=40560.65722061269&xp=42396.0789533435&tool=tracingtool&sid0=1&s0=4.5&help=true&layout=h(XY,%20%7B%20type:%20%22neuron-search%22,%20id:%20%22neuron-search-1%22,%20options:%20%7B%22annotation-name%22:%20%22papers%22%7D%7D,%200.6)

Find them via Neuron Search (icon with a "?").

The "Construction time" is wrong (see "Summary info" of the Selection Table) because these neurons were imported from #TrakEM2. Old enough to predate the #CATMAID software!
#neuroscience

CATMAID

Show threadAlbert CardonaNov 25, 2022

#TrakEM2 runs as a plugin of #FijiSc https://fiji.sc/ and in fact motivated the creation of the #FijiSc software in the first place, to manage its many dependencies and facilitate distribution to the broader #neuroscience community.

#TrakEM2 was founded in 2005, when TB-sized datasets were rare and considered large. Largest dataset I've successfully managed with #TrakEM2 was ~16 TB. For larger volumes see #CATMAID.

For 3D visualization #TrakEM2 uses the 3D Viewer https://imagej.net/plugins/3d-viewer/

Fiji: ImageJ, with "Batteries Included"

Fiji: A batteries-included distribution of ImageJ.

Albert CardonaNov 25, 2022

#introduction To fill in my profile tags, a thread:

#TrakEM2 open source software mostly for #connectomics, and supports manual and automatically montaging and aligning overlapping 2D image tiles (with #SIFT features and rigid or elastic transformation models), and reconstructing by painting volumes or tracing branched neuronal arbors neurons plus synapses to map a #connectome from #vEM (volume electron microscopy).

See: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038011

Git repository at: https://github.com/trakem2/

TrakEM2 Software for Neural Circuit Reconstruction

A key challenge in neuroscience is the expeditious reconstruction of neuronal circuits. For model systems such as Drosophila and C. elegans, the limiting step is no longer the acquisition of imagery but the extraction of the circuit from images. For this purpose, we designed a software application, TrakEM2, that addresses the systematic reconstruction of neuronal circuits from large electron microscopical and optical image volumes. We address the challenges of image volume composition from individual, deformed images; of the reconstruction of neuronal arbors and annotation of synapses with fast manual and semi-automatic methods; and the management of large collections of both images and annotations. The output is a neural circuit of 3d arbors and synapses, encoded in NeuroML and other formats, ready for analysis.

Show threadAlbert CardonaNov 10, 2022

@manlius Yes, a lot, but generated mostly with #CATMAID which is more purpose-built for #connectomics.

An early reconstruction of a neural circuit done with #TrakEM2 was by Davi Bock et al. 2011 on the mouse visual cortex, "Network anatomy and in vivo physiology of visual cortical neurons" https://www.nature.com/articles/nature09802

Another one with #TrakEM2 was by Dan Bumbarger et al. 2013 "System-wide rewiring underlies behavioral differences in predatory and bacterial-feeding nematodes" where they compared #celegans with another nematode, #pristionchus pacificus that has the exact same amount of neurons but connected differently https://www.sciencedirect.com/science/article/pii/S0092867412015000

Later ones with #CATMAID include:

The polychaete worm #Platynereis by @jekely 's group, "Whole-animal #connectome and cell-type complement of the three-segmented Platynereis dumerilii larva" Verazto et al. 2020 https://www.biorxiv.org/content/10.1101/2020.08.21.260984v2.abstract

And all of ours in #Drosophila larva. See the #VirtualFlyBrain server which hosts the #vEM of the whole central nervous system and lists all the neurons included in each published paper (currently 23), shared among the papers and all connecting to each other: https://l1em.catmaid.virtualflybrain.org/?pid=1&zp=108250&yp=82961.59999999999&xp=54210.799999999996&tool=tracingtool&sid0=1&s0=2.4999999999999996&help=true&layout=h(XY,%20%7B%20type:%20%22neuron-search%22,%20id:%20%22neuron-search-1%22,%20options:%20%7B%22annotation-name%22:%20%22papers%22%7D%7D,%200.6)

The 24th will come soon, featuring the complete whole #Drosophila larval brain with ~2,500 neurons. It's under review.

Network anatomy and in vivo physiology of visual cortical neurons - Nature

To date, various aspects of connectivity have been inferred from electron microscopy (EM) of synaptic contacts, light microscopy of axonal and dendritic arbors, and correlations in activity. However, until now it has not been possible to relate the complex structural wiring between neurons to the function of individual cells. Using a combination of functional imaging and three-dimensional serial EM reconstruction at unprecedented scale, two papers now describe the connectivity of single cells in the mouse visual system. This study investigates the connectivity of inhibitory interneurons in primary visual cortex.

Nature