Electron-Light Microscopy tools for Janelia
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README.md

elm

Electron-Light Microscopy tools for Janelia

If you are using this tool in your work, please do not forget to cite John Bogovic's paper where he first introduces the underlying BigWarp tool:

JA Bogovic, P Hanslovsky, A Wong, S Saalfeld, "Robust registration of calcium images by learned contrast synthesis", In Biomedical Imaging (ISBI), 2016 IEEE 13th International Symposium on, 1123-1126, DOI: 10.1109/ISBI.2016.7493463.

This project enables visualization of light microscopy in the space of a particular version of FAFB (internal to Janelia only). Any images in the space of the fly light nc82 template (size: 1450 x 725 x 436 ) can be visualized.
The transformation was generated manually using BigWarp which in turn is built upon BigDataViewer.

See also elmr, for interaction between the CATMAID web application and the R Neuroanatomy Toolbox package.

Announcements

  • 2018-Apr-18 - Update to v14.
  • 2017-Mar-09 - Use Davi Bock's refinements for v13.
  • 2017-Mar-08 - Use Davi Bock's new landmarks for v13.
  • 2016-Dec-16 - ELM now uses FAFB v13 by default.
  • 2016-Apr-01 - ELM now uses FAFB v12 by default.
  • 2016-Feb-22 - Landmark improvements thanks to Davi Bock.
  • 2016-Feb-09 - ELM now uses FAFB v11 by default.

Installation

Two alternatives:

  1. Using GIT:

Clone this repository into your fiji plugins folder.

cd <your fiji folder>/plugins
git clone https://github.com/saalfeldlab/elm.git
  1. Download and copy:

Download the zipped archive and extract into

<your fiji folder>/plugins/elm-master/

or

<your fiji folder>/plugins/elm/

Running

  • After installation, the script can be accessed from the Fiji menu by:
    • Plugins > elm > ELM
  • Use the dialog to select an image to warp into FAFB space
    • Note: it must be coregistered to the JFRC2013 template nc82 stack

    • If "Auto discover" is selected, ELM will open the selected image and, if the selected image has only one channel, will search for other channels:

      1. in the same folder,
      2. with the same extension, and
      3. the same size as the selected image.

      This is the way to open multi-channel exports that come out as separate files.

Hotkeys

  • The 'K' key will open the FAFB stack in CATMAID at the location displayed in the current window.
  • The 'C' key will point ELM viewer to a location in the stack corresponding to a given CATMAID URL.
  • The 'L' key (press and hold ) will display the name of the label under the mouse cursor if compartment labels are loaded.

Compartment labels

As of 20 January 2016, ELM includes pointers to compartment labels maps. Label maps are not loaded by default, but one can be selected with the radio buttons:

  • DPX - a label map internal to Janelia.
  • VFB - labels from the Virtual fly brain
    • These were manually registered to the high-resolution template by John Bogovic (improvements welcome).

If a label map is selected, it is visible by default. This can be changed using the Visibility and Grouping dialog (F6 (moving) and F7 (target)). See details on the big data viewer page.