Difference between revisions of "TrakEM2 tutorials"

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See the [http://www.ini.uzh.ch/~acardona/movies/arealist-create-and-edit.mp4 the "area list" video tutorial here].
 
See the [http://www.ini.uzh.ch/~acardona/movies/arealist-create-and-edit.mp4 the "area list" video tutorial here].
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See als the list of [http://www.ini.uzh.ch/~acardona/trakem2_manual.html#edit_arealist key bindings for AreaList].
  
 
This video tutorial was made by Albert Cardona. To visualize it, you need a mp4 player.
 
This video tutorial was made by Albert Cardona. To visualize it, you need a mp4 player.
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See the [[TrakEM2 align sections tutorial|aligning video tutorial here]].
 
See the [[TrakEM2 align sections tutorial|aligning video tutorial here]].
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See also the feature extraction and alignment [http://www.ini.uzh.ch/~acardona/howto.html#sift_parameters parameters explained].
  
 
This video tutorial was made by Javier Cabrera-Chaves and edited by [[User:iarganda|Ignacio Arganda-Carreras]] using [http://www.debugmode.com/wink/ Wink 1.5 for linux]. To navigate, use the green arrows to go forward and backward in the slide-show.
 
This video tutorial was made by Javier Cabrera-Chaves and edited by [[User:iarganda|Ignacio Arganda-Carreras]] using [http://www.debugmode.com/wink/ Wink 1.5 for linux]. To navigate, use the green arrows to go forward and backward in the slide-show.
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See the [[TrakEM2 measurements tutorial|measurements video tutorial here]].
 
See the [[TrakEM2 measurements tutorial|measurements video tutorial here]].
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See also [http://www.ini.uzh.ch/~acardona/trakem2_manual.html#measure_arealist AreaList measurements] in the TrakEM2 manual, with figures.
  
 
This video tutorial was made by Javier Cabrera-Chaves and edited by [[User:iarganda|Ignacio Arganda-Carreras]] using [http://www.debugmode.com/wink/ Wink 1.5 for linux]. To navigate, use the green arrows to go forward and backward in the slide-show.
 
This video tutorial was made by Javier Cabrera-Chaves and edited by [[User:iarganda|Ignacio Arganda-Carreras]] using [http://www.debugmode.com/wink/ Wink 1.5 for linux]. To navigate, use the green arrows to go forward and backward in the slide-show.

Revision as of 08:29, 18 September 2009

Video tutorial on the basic recipe for TrakEM2

TrakEM2 basic tutorial

This is the basic tutorial for TrakEM2. If you are new to TrakEM2, please start by watching this tutorial. It includes:

  • Importing an image stack.
  • Registering stack slices manually, using color overlays and affine transforms.
  • Defining a template tree structure for your segmentations.
  • Segmenting cells across multiple sections.
  • 3D visualization.


See the basics video tutorial here.

This video tutorial was made by Javier Cabrera-Chaves and edited by Ignacio Arganda-Carreras using Wink 1.5 for linux. To navigate, use the green arrows to go forward and backward in the slide-show.

Video tutorial on segmenting/outlining objects over multiple sections in 3D

TrakEM2 brushing
  • How to use the PEN tool with "area lists" segmentation type (paint an area, flood-fill, erase, flood-erase).
  • How to use ROIs (selections like polygon and freeroi) to edit "area lists".


See the the "area list" video tutorial here.

See als the list of key bindings for AreaList.

This video tutorial was made by Albert Cardona. To visualize it, you need a mp4 player.



Video tutorial on aligning sections

  • Automatically registering sections.
  • Selecting feature extraction parameters.


See the aligning video tutorial here.

See also the feature extraction and alignment parameters explained.

This video tutorial was made by Javier Cabrera-Chaves and edited by Ignacio Arganda-Carreras using Wink 1.5 for linux. To navigate, use the green arrows to go forward and backward in the slide-show.

Video tutorial on manual segmentation modes

How to manually segment cells using the 3 segmentation modes:

  • Overlap: multiple arealists can coexist in space (the normal mode; arealists are independent).
  • Exclude: when painting in an arealist, do not allow paint to ocurr over any other existing arealist.
  • Erode: when painting in an arealist, paint in the current but erase any other arealist.


See the segmentation modes video tutorial here.

This video tutorial was made by Javier Cabrera-Chaves and edited by Ignacio Arganda-Carreras using Wink 1.5 for linux. To navigate, use the green arrows to go forward and backward in the slide-show.

Video tutorial on semi-automatic segmentation

  • How to segment cells by only one click.
  • Fast marching method tool in TrakEM2.
  • Selecting segmentation parameters.


See the semi-automatic segmentation video tutorial here.

This video tutorial was made by Javier Cabrera-Chaves and edited by Ignacio Arganda-Carreras using Wink 1.5 for linux. To navigate, use the green arrows to go forward and backward in the slide-show.

Video tutorial on measuring surfaces and volumes

  • Extract information from TrakEM2 project objects.


See the measurements video tutorial here.

See also AreaList measurements in the TrakEM2 manual, with figures.

This video tutorial was made by Javier Cabrera-Chaves and edited by Ignacio Arganda-Carreras using Wink 1.5 for linux. To navigate, use the green arrows to go forward and backward in the slide-show.

Video tutorial on adding sections/layers to an existing project

  • Open an image sequence as a virtual stack in Fiji.
  • Calibrate the virtual stack.
  • Import the virtual stack into TrakEM2 as a sequence of layers (sections), one image per layer.

In the tutorial, the layers are imported following an existing set of layers, i.e. concatenating to enlarge the collection of sections.

See the add more layers video tutorial here.

This video tutorial was made by Javier Cabrera-Chaves and edited by Ignacio Arganda-Carreras using Wink 1.5 for linux. To navigate, use the green arrows to go forward and backward in the slide-show.

Video tutorial on saving a project

  • Saving a TrakEM2 project into an .XML file.

See the saving project video tutorial here.

This video tutorial was made by Javier Cabrera-Chaves and edited by Ignacio Arganda-Carreras using Wink 1.5 for linux. To navigate, use the green arrows to go forward and backward in the slide-show.