Plugins Menu

This menu allows access to custom plugins.

The plugins should be placed under mib->Plugins directory as PLUGIN_GROUP_NAME/PLUGIN_NAME, where PLUGIN_GROUP_NAME is a directory with similarly grouped plugins. PLUGIN_NAME - is a directory with the actual plugin. The name of controller for each plugin should be formed as: PLUGIN_NAMEController, for example mytestController.m. So the full filename may look like this:

c:\MATLAB\Scripts\mib\Plugins\MyPlugings\myPlugin\myPluginController.m

Please check the contents of Plugins->Tutorials for examples. See more in the corresponding tutorials .

File processing
Intensity analysis
Organelle analysis
Plasmodesmata
Tutorials

File processing

Image converter - a plugin for bulk conversion of files from one format to another. A small video tutorial is available via these links: https://youtu.be/Xu1waZ913bE and https://youtu.be/X2XE5EZCsiI *

Intensity analysis

Plugins for analysis of intensities in images

Triple area intensity - a plugin to calculate intensity in 3 related areas in images and calculate the ratios. Click the Help button in the plugin for details

Organelle analysis

Analysis of biological objects

MCcalc, a plugin for detection of contacts and calculation of distance distributions from TEM images. See more in the the full MCcalc workflow presented on http://mib.helsinki.fi/tutorials_tools.html
Surface Area 3D - calculation of surface areas for planar structures from MIB models. Use the Help button inside the plugin for details

Plasmodesmata

Plugins for analysis of plasmadesmata in roots of Arabidopsis thaliana. For details please follow to this publication: Paterlini A, Belevich I, Jokitalo E, Helariutta Y., Computational Tools for Serial Block Electron Microscopy Reveal Plasmodesmata Distributions and Wall Environments, Plant Physiol. 2020 Sep;184(1):53-64. doi: 10.1104/pp.20.00396. Epub 2020 Jul 23. https://pubmed.ncbi.nlm.nih.gov/32719057

Tutorials

Demo examples from the tutorials section: http://mib.helsinki.fi/tutorials_programming.html