Catmaid

The Collaborative Annotation Toolkit for Massive Amounts of Image Data (CATMAID) is a web companion to the TrakEM2 software (Cardona, 2006) for management, registration and analysis of large-scale ssTEM datasets

1: L1 EM Catmaid Dataset

2: FAFB Catmaid Dataset

3: FANC Catmaid Dataset

Documentation

CATMAID documentation

@catmaid

Intro

## Catmaid Datasets

The Virtual Fly Brain (VFB) hosts many catmaid EM connectomic reconstruction projects published data so you can explore the fine details using catmaids as well as the data being intergrated and discoverable in VFB.

1 - L1 EM Catmaid Dataset

Drosophila Larval (L1) CNS Tracing by Albert Cardona’s lab at HHMI Janelia Research Campus and collaborators.

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@albertcardona

Dr Albert Cardona - Department of Physiology, Development and Neuroscience, University of Cambridge

Dr Albert Cardona - Janelia, HHMI

VFB L1EM CATMAID Server

VFB L1EM CATMAID API

FAFB Datasets inside VFB

Projects

[
  {
    "id": 1,
    "stackgroups": [],
    "stacks": [
      {
        "comment": "L1 CNS ssTEM at 3.8x3.8x50 nm of whole Drosophila 1st instar larval CNS",
        "id": 1,
        "title": "L1 CNS 0-tilt"
      }
    ],
    "title": "L1 CNS"
  }
]

2 - FAFB Catmaid Dataset

FAFB is a sparse connectome of the complete adult cephalic brain. This group is working towards building the first dense synaptic-resolution connectome of an adult fly’s central nervous system (brain and ventral nerve cord). This is part of an international collaboration with HHMI Janelia Research Campus in the US, the MRC LMB in Cambridge and the University of Oxford Centre for Neural Circuits and Behaviour, funded by the Wellcome. The electron microscopy volumes that underpin our neural reconstruction are generated at Janelia.

png

Drosophila connectomics group at the Department of Zoology

TEMCA2 - A full adult fly brain (FAFB), imaged at synaptic resolution

VFB FAFB CATMAID Server

VFB FAFB CATMAID API

FAFB Datasets inside VFB

Projects

[
  {
    "id": 1,
    "stackgroups": [],
    "stacks": [
      {
        "comment": "",
        "id": 1,
        "title": "fafb"
      }
    ],
    "title": "Adult Brain"
  }
]

3 - FANC Catmaid Dataset

FANC is a sparse connectome of the adult Ventral Nerve Cord (VNC). Reconstruction of motor control circuits in adult Drosophila using automated transmission electron microscopy; Jasper S. Phelps, David Grant Colburn Hildebrand, Brett J. Graham, Aaron T. Kuan, Logan A. Thomas, Tri M. Nguyen, Julia Buhmann, Anthony W. Azevedo, Anne Sustar, Sweta Agrawal, Mingguan Liu, Brendan L. Shanny, Jan Funke, John C. Tuthill, and Wei-Chung Allen Lee. https://doi.org/10.1016/j.cell.2020.12.013

png

Reconstruction of motor control circuits in adult Drosophila using automated transmission electron microscopy

VFB FANC CATMAID Server

VFB FANC Aligned to JRC2018 VNC Female template on CATMAID Server

VFB FAFB CATMAID API

FANC Neurons inside VFB

Projects

[
  {
    "id": 1,
    "stackgroups": [],
    "stacks": [
      {
        "comment": "",
        "id": 1,
        "title": "VNC XY"
      }
    ],
    "title": "Adult VNC"
  },
  {
    "id": 2,
    "stackgroups": [],
    "stacks": [
      {
        "comment": "",
        "id": 3,
        "title": "JRC2018_VNC_FEMALE"
      }
    ],
    "title": "JRC2018_VNC_FEMALE"
  }
]