MIB joins the forum

matlab
mib

#1

Dear colleagues,

we are glad to announce that Microscopy Image Browser (MIB) has joined the image.sc forum as a community partner. It fills exciting be a part of this community and we are looking forward into it.

For those, who are not familiar with MIB, I would like to take this opportunity to introduce it in brief. MIB is a software package for image processing, segmentation, analysis and visualization of multidimensional datasets. It was designed for efficient work with 3D electron microscopy datasets, but we also successfully applied it in various light microscopy projects. MIB is written in Matlab and distributed as Matlab-compatible and standalone (compiled for Windows and MacOS) packages. The original software was published in 2016 in PLOS Biology but it is still under the continuous development.

Main features:

  • Generation of multi-dimensional image stacks (height:width:colors:depth:time) from up to 100 image and video formats, OMERO server, Fiji and Imaris
  • Virtual stacking mode for browsing datasets larger than available memory
  • Large collection of image processing, manual and semi-automatic segmentation tools
  • Quantification of 2D/3D objects
  • Export of images or models directly to Fiji and Imaris or as files in Matlab, Amira, IMOD, STL, TIF, NRRD, Fiji BigDataViewer, Ilastik formats
  • Direct 3D visualization using isosurfaces and volume rendering, Fiji 3D viewer and Imaris
  • Customizable Undo system
  • Customizable Keyboard shortcuts
  • Extendable with custom plugins
  • Licensed under the GNU General Public License v2

Please check the list of all features with brief video demonstrations and tutorials on various topics.
MIB can be downloaded from the dedicated website or github.

Best regards,
Ilya Belevich and MIB team


#2

just a point that maybe I am not getting, how can it be open source if it’s Matlab based?


#3

@emartini,
the source is there, so it can be reused and modified.


#4

While Matlab itself isn’t open source, you can still publish your own Matlab code under an open-source license. The matter becomes interesting when choosing GPL (which requires to also provide the source for all dependencies), here are some interesting discussions:

From the above link:

The GPL requires anyone who redistributes your code or derivatives thereof to include source code not only for your code but also for any libraries it is linked to, which might mean that others have to redistribute the Matlab source code in order to copy yours, which of course they couldn’t do, so in that case it would be the same as giving use rights and no copying rights.



@Ilya_Belevich how about licensing your project with an LGPL or BSD license instead?


#5

@imagejan,
thank you for pointing this out, it is an interesting nuance, I will recheck that.