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IMOD

About:

"IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections."

IMOD is a program I have spent countless hours using to generate data for my PhD. The program was developed by the University of Colorado in Boulder and during my PhD I was fortunate enough meet the primary author of the program, Dr David Mastronarde, who showed me how I could create my own "plugin windows" for the main IMOD interface "3dmod".

Since then, I have developed several small plugin windows which, with the help of David, have now been incorporated into the IMOD. On this page I have provided training videos and a information about each of my four main plugins:

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Videos:

WARNING: Videos may take several minutes to load

  • Drawing Tools and Interpolator - Overview **** - [youtube] - a quick showcase of how to use the different drawing tools, and how they work in parallel with Interpolator without going into too much details. The rest you should figure out for yourself! (2 mins)
  • Name Wizard - Overview ** - [youtube] - an overview of my latest plugin (Name Wizard) showing how it works and how it can help you quickly rename and recolor all your objects quickly. (6 mins)
  • Installing IMOD on Windows - [youtube] - NOTE: has become somewhat obsolete, and IMOD now features a clickable (.exe) installer for Windows 32-bit and 64-bit. (4mins)

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Plugins I have created:

Bead Helper

This plugin is designed to assist in the speedy refinement of fiducial models - allowing you to quickly identify and correct bad points. "Bead Helper" is designed to compliment the functionality of "Bead Fixer" by providing useful visual aids and tools which can be used to rapidly rectify or delete bad contours - i.e. contours where the fiducial marker has tracked poorly. If tracking goes well you probably won't need Bead Helper, but in situations where tracking proves problematic Bead Helper has many tools which may be able to help. (more)

Drawing Tools

This plugin provides a set of drawing tools which allows you to rapidly draw, modidy and erase contours. To use these tools make sure 3dmod is on "Model" mode, the "Drawing Tools" plugin window is open and you've selected the "Draw Mode" you wish to use. Notice in the Zap window that many of the tools use a red "sculpt circle", the size of which can be changed using mouse wheel. (more)

Interpolator

This plugin allows for rapid segmentation of surfaces by automatically generating "interpolated" contours between the "key" contours which you have manually drawn. Each time you add a new contour, press [Enter] (instead of [n]) and the program will generate interpolated contours between any connected key contours either side of the contour you have just added or modifed.
Contours are "connected" if they are within "Z Bridge" slices of each other and the computer believes they are part of the same surface as according to the selected "surface method". The shape of interpolated contours depends on which "interpolation type" you have selected. (more)

Name Wizard

I designed this plugin to encourage the use of proper and consistent names and colors of objects in IMOD. Students labelling objects incosistenly or not at all is a big problem, but using this plugin users can use an autocomplete to select from a huge list of "proper names" which tie in with the "Neurolex" and "Gene Ontology" databases of accepted names and unique identifiers for each (read more about this problem). This list is loaded from a CSV (comma seperated value) file which can be modified to changes hyperlinks, preferred colors or add names.  By default there are just over 200 entries which were taken from the NeuroLex "Subcellular Parts Table". In addition to auto-complete, this plugin helps rapidly enter and verify that all names match the entries in the CSV file. There are also options here to manage objects by reordering, deleting, merging or splitting. Thus, if you are serious about making your group use consistent labels, I recommending installing the same CSV and installing Name Wizard on all computers in your group. (more)

Name Wizard plugin

NOTE: I have written more on the topic of creating IMOD plugins here.