Microscopy Image Browser updated to 2.60

Microscopy Image Browser was today updated to version 2.60. The update is focused on the automation of image processing routines by arranging them into protocols.

The compiled version of MIB was made for R2019b, which is the very recent release of Matlab.

Update details:

  • Added the Batch mode for repetitive processing of images ( Menu->File->Batch processing )
  • Added visualization of models using Matlab Volume Viewer app ( Menu->Models->Render model->Matlab volume viewer , R2019 or newer, Matlab version only)
  • Added Drag & Drop materials to the segmentation tools ( Segmentation panel->Drag and Drop materials )
  • Added content-aware fill using coherence transport ( Menu->Image->Tools for images->Content-aware fill , R2019a and newer)
  • Added debris removal tool to automatically or menually remove debris from volumetric datasets ( Menu->Image->Tools for images->Debris removal )
  • Added alignment of color channels using landmark multi points ( Menu->Dataset->Alignment->Algorithm:Color channels, multi points )
  • Added use of Oriented FAST and rotated BRIEF (ORB) points for automatic alignment ( Menu->Dataset->Alignment , R2019 or newer)
  • Added optional correction for instant jumps during running average correction of the drift alignment algorithm
  • Added possibility to add material name and object id during export of quantitation results from the Statistics Dialog to the annotation layer
  • Added export of results from the Statistics Dialog to comma-separated values
  • Added copy to the system clipboard the columns from the the Statistics Dialog (right mouse click over the table and select Copy column(s) to clipboard)
  • Added batch modification of values and coordinates for the annotations
  • Added 4D options to “Material to Selection” and “Material to Mask” options for the context menu of the Segmentation table
  • Added calculation of quantile for automatic contrast stretching ( View settings->Display->Right click over the min/max buttons )
  • Added ( "Ctrl+E ) key shortcut to toggle between current and previous image container
  • Added export of graphs from the graphcut workflow to 3D Lines for visualization
  • Rewritten Image arithmetics to include mask, model, and selection layers ( Menu->Image->Tools for images->Image arithmetic... )
  • Updated use of xlswrite, for R2019a or newer writecell function will be used
  • Updated data conversion from 32-bit to 8- and 16-bit; from 8-bit to 16-bit
  • Updated Bio-Formats to 6.2.1 (Requires Matlab R2017b or newer)

MIB can be updated from MIB->Menu->Help->Check for update or downloaded directly from the MIB website .
Available as Matlab code, or as compiled binaries for Windows and MacOS.

Awesome! Looking forward to test the new features over the weekend.

I just noticed that some of the Youtube videos of the new features (Links on http://mib.helsinki.fi and http://mib.helsinki.fi/downloads.html) are marked as private and thus are not accessible. Just wanted to let you know about that.

Cheers
Stefan

Hi Stefan,
thank you for the note - indeed, I forgot to change them to public - highly appreciated!
Now it is fixed.
I personally recommend to test the batch mode - it is very useful. It can also (I think that part is not demonstrated in the brief video) record operations done in MIB and automatically add them to the protocol.
Best regards,
Ilya

You, sir, are a rock star!

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