@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!

@adredish @neuralreckoning @brembs @ScholarNexus

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

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

@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.

@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:

@carrerassanahuja També ho pots fer amb #TrakEM2 i #FijiSc — però és més tècnic. Igualment de codi obert.

@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

#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/

#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/

@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.

@leoboeger The famous #pristionchus! Proud to have helped Dan Bumbarger [1] back in Zurich in 2010 or so when he visited me to learn how to register his serial sections with #TrakEM2. It’s been a while.

[1] Bumbarger et al. 2013 https://www.sciencedirect.com/science/article/pii/S0092867412015000

@thor @riedl The academic world has a history of using open source software… and of creating it. My own: #FijiSc #TrakEM2 #CATMAID: https://qoto.org/@albertcardona/109269348386409802

Now onto #FijiSc: Fiji is a recursive acronym meaning "Fiji is just ImageJ" https://fji.sc (and the paper https://www.nature.com/articles/nmeth.2019 ) –and #ImageJ is a #java open source software for image processing https://imagej.nih.gov/ij/index.html written by Wayne Rasband from the #NIH Research Branch.

An analogy: think of ImageJ as the kernel and Fiji as the rest of the operating system.

#FijiSc brings to #ImageJ:
(1) a package manager to install and update plugins, and that crucially enables reproducible science by exporting the whole set of plugins and libraries as an executable;
(2) a Script Editor https://imagej.net/scripting/script-editor supporting many languages (#python, #groovy #ruby #scala #clojure and more), all with access to a huge collection of #JVM libraries;
(3) huge amount of libraries such as #ImgLib2, #JFreeChart for plotting, for GUIs, etc.

There are many, many plugins. A tiny sample:

Machine learning-based image segmentation:
- #LabKit https://imagej.net/plugins/labkit/
- #WEKA Trainable Segmentation https://imagej.net/plugins/tws/index

3D/4D/ND Visualization:
- 3D/4D Viewer #3DViewer https://imagej.net/plugins/3d-viewer/index with ray-tracing, orthoslices, volume rendering, and more
- #BigDataViewer #BDV https://imagej.net/plugins/bdv/index for interactively navigate N-dimensional image volumes larger than RAM

Image registration and serial section alignment:
- #BigStitcher for registering 3D/4D tiled datasets, with multiview deconvolution and more https://imagej.net/plugins/bigstitcher/index
- #TrakEM2 for montaging in 2D and alinging in 3D collections of serial sections, typically from #vEM (volume electron microscopy) https://syn.mrc-lmb.cam.ac.uk/acardona/INI-2008-2011/trakem2.html
- #mpicbg libraries for extracting #SIFT and #MOPS features, then finding feature correspondences and estimating rigid and elastic transformation models https://www.nature.com/articles/nmeth.2072

Summarizing #FijiSc is impossible. See the online forum where questions find answers by the hand of the broader community of users and developers https://forum.image.sc/

To fill in my profile tags, a thread:

#TrakEM2 is open source software mostly for #connectomics (but found uses well beyond), and provides the means for both manual and automatic montaging and aligning overlapping 2D image tiles (with #SIFT features and rigid or elastic transformation models), and then reconstructing with mostly manual means–by painting with a digital brush–the volumes of structures of interest, as well as trace the branched arbors of e.g., neurons and annotate their synapses, therefore mapping a #connectome from #vEM (volume electron microscopy).

#TrakEM2 paper at https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038011

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

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

As software, #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 therefore facilitate distribution to the broader #neuroscience community.

#TrakEM2 was founded in 2005, when terabyte-sized datasets were rare and considered large. The largest dataset that I've successfully managed with #TrakEM2 was about 16 TB. For larger datasets, see #CATMAID below.

Above, my #introduction of interests. Here, who I am, what I do: a neuroscientist at the #MRCLMB and University of Cambridge, UK, studying the neural circuit basis of behavior, originally in #Drosophila but now also in #cephalopods (#pygmysquid #Idiosepius), the lancelet #Amphioxus and other animals. Our main approach: whole brain #connectomics with #vEM (volume electron microscopy) as the basis for computational modeling to guide neuronal activity perturbation and monitoring experiments with #optogenetics and #electrophysiology (#ephys for short).
Once upon a time I founded the #ImageJ -based #TrakEM2 software for image registration and neuronal arbor reconstruction and annotation, which spurred founding the #FijiSc (https://fiji.sc) image processing software, and later the #CATMAID web-based software for #connectomics.
Always open to inquires from prospective students and postdocs, and collaborations.