Mosaicing

Mosaicing Tools

Open-source software tools to build mosaics of partially overlapping images

PROJECT MicroMos

MicroMos is an open-source software tool for automatically building an image mosaic by stitching at pixels or sub-pixel accuracy a set of partially overlapping images manually acquired with a widefield microscope, typically without a motorized stage. Different algorithm configurations can be adopted to stitch the images, also correcting for vignetting effects. No prior information is required. The only assumption regards the objects present in the images: they must be still, non-deformable. The final mosaic has the same pixel resolution of the input images.

Please, find more details in:

F. Piccinini, M. Pierini, E. Lucarelli, A. Bevilacqua, Semi-quantitative monitoring of confluence of adherent mesenchymal stromal cells on calcium-phosphate granules by using widefield microscopy images. Journal of Materials Science: Materials in Medicine, May 2014. Download
F. Piccinini, A. Bevilacqua, E. Lucarelli, Automated image mosaics by non-automated light microscopes: the MicroMos software tool. Journal of Microscopy, September 2013. Download
F. Piccinini, E. Lucarelli, A. Gherardi, A. Bevilacqua, Multi-image based method to correct vignetting effect in light microscopy images. Journal of Microscopy, October 2012. Download
F. Piccinini, A. Bevilacqua. Colour vignetting correction for microscopy image mosaics used for quantitative analyses. BioMed Research International, June 2018. Download

LAST VERSION:

MicroMos Version 3.0 (*), License. The first version endowed with a Graphical User Interface (GUI) and a module for manually defining the shifts between the images to be stritched.

OLDER VERSIONS:

MicroMos Version 2.0 (*), License. To build mosaics of brightfield, phase-contrast and fluorescent images.
MicroMos Version 1.0 (*), License. To build mosaics of brightfield and phase-contrast images only. (click on "Supplementary Material" section)

(*) Requirements: MATLAB R2015a and Image Processing Toolbox 9.2 or later versions.

PROJECT GridMos

Nowadays, the manual cell counting, performed directly by looking through the microscope’s oculars by using a tally counter and a hemocytometer, still is the gold standard method to count Live and Dead cells (Trypan Blue is typically used to stain the dead cells). However, performing the cell counting by tagging the cells in a steady image mosaic increases the reliability of the counts performed. Unfortunately, to build a mosaic of a hemocytometer's grid shows some problem due to the repeated patterns (i.e., the squared blocks of the grid). GridMos is an open-source software tool conceived to build an image mosaic of a hemocytometer's grid. It is optimized to build the mosaic starting from a sequence of overlapping images previously acquired. The Graphical User Interface (GUI) implemented makes GridMos a very user-friendly software tool.

Please, find more details in:

F. Piccinini, A. Tesei, G. Paganelli, W. Zoli, A. Bevilacqua, Improving reliability of live/dead cell counting through automated image mosaicing. Computer Methods and Programs in Biomedicine, December 2014. Download

DOWNLOAD SOFTWARE:

GridMos Version 1.0 (*), License.
Sample set 01: 11 tiff images, 1600x1200 pixels, RGB, acquired in brightfield by using a 4x objective. Description: hemocytometer's grid with cells stained by using Trypan blue. The background of the images is particularly blue.
Sample set 02: 11 tiff images, 1600x1200 pixels, RGB, acquired in brightfield by using a 4x objective. Description: hemocytometer's grid with cells stained by using Trypan blue. The background of the images is really bright (over-exposed).
Sample set 03: 11 tiff images, 1600x1200 pixels, RGB, acquired in brightfield by using a 4x objective. Description: hemocytometer's grid completely empty (no cell seeded, no culture medium inside the grid).

(*) Requirements: MATLAB 2009b and Image Processing Toolbox 8.1 or later versions.

CONTACT US

Filippo Piccinini
Advanced Research Center on Electronic Systems (ARCES), University of Bologna, Italy
[email protected]

Alessandro Bevilacqua
Advanced Research Center on Electronic Systems (ARCES), University of Bologna, Italy
Department of Computer Science and Engineering (DISI), University of Bologna, Italy
[email protected]

To obtain the password to download and open the compressed folders, please send an email to: [email protected] -->