SOFTWARE TOOLS:

 

• Advanced Cell Classifier, for classifying cells in high-content screening images. https://cellclassifier.com/

• AnaSP, software suite to segment brightfield images of multicellular spheroids. https://sourceforge.net/p/anasp

• AND-Tool, Matlab tool for segmenting nuclei in 2D widefield images stained with DAB. https://sourceforge.net/p/andtool/

• CellTracker, for tracking in 2D cells cultured in vitro. http://celltracker.website

• CIDRE, for correcting the illumination field of microscopy images. http://www.nature.com/nmeth/journal/v12/n5/full/nmeth.3323.html

• Colori-DT, for quantitatively compare colour images. https://sourceforge.net/p/colori-dt/

• Colour Deconvolution 2, ImageJ/Fiji plugin for stain unmixing in RGB histological images. Prof. Gabriel Landini webpage

• CometAnalyser, for quantitative comet assay analysis of silver stained and fluorescence images. https://sourceforge.net/p/cometanalyser

• DS4H Image Alignment, ImageJ/Fiji plugin for aligning images based on markers manually defined. www.filippopiccinini.it/DS4H-IA.html

• F-Tracker3D, for tracking in 3D fluorescent particles imaged with a confocal/light-sheet microscope. https://sourceforge.net/p/f-tracker3d

• MicroMos, for building a panorama, starting from a set of overlapping images. www.filippopiccinini.it/Mosaicing/index.html

• ReViMS, for cancer spheroids Reconstruction and Visualization using Multiple Sections. https://sourceforge.net/p/revims

• ReViSP, for cancer spheroids Reconstruction and Visualization using a Single Projection. https://sourceforge.net/p/revisp

• TDSFT, for “averaging” (i.e., process and fuse) multiple 2D black&white segmentations. https://sourceforge.net/p/tdsft

• 3D-Cell-Annotator, MITK plugin for segmenting single cells in 3D datasets. www.3d-cell-annotator.org

OTHER MATERIAL:

 

To obtain the passwords to open the following compressed folders, please send an email to This email address is being protected from spambots. You need JavaScript enabled to view it. specifiying the name of the file you are interested in.

1. Vignetting estimation tool for light microscopy: to estimate the vignetting function and to correct the vignetting effect starting from a set of images acquired with a light microscope.

2. Method for extending the depth of focus of the microscope: to reconstruct the in-focus 2D image starting from a set of images acquired at different focus positions simply moving the microscope along the z-direction.

3. Watershed segmentation for binary images: to perform the watershed segmentation on binary images (black and white). The result obtained is similar to the one of the watershed function implemented in ImageJ. This function is typically used to separe touching cells.

4. Image threshold manually adjusted: program with user-friendly GUI interface to threshold a large set of images in a short time through manually adjusting the threshold value for each image to be processed.

5. UQIN: index to assess N-image fusion in light microscopy without requiring a reference ground truth. UQIN is an extension of the Universal Quality Index and it is able to assess the quality of an image fusion method starting from the single images used to obtain the final result. It does not require a reference ground truth image.

6. Shift by Phase Correlation: to compute the x-y shift with pixel accuracy between two input images of the same size. The two input images must be a shifted copy of the same scene. Rotations can not be managed. The shift between the two input images must be at maximum 95%.

7. White Balancing: to balance the histograms of the three RGB channels of in RGB input image. The White Balancing can be performed according to different algorithm configurations simply using an input flag.

8. Image contrast stretching: to adjust the contrast of an input image directly defining the output minimum and maximum intensity values.

9. Mean Squared Error (MSE), Signal to Noise Ratio (SNR), Universal Quality Index (UQI): to compute standard metric indexes between two input images. NaN values maybe present in the input images are correctly discarded in the computation.

10. Triangle thresholding for grey images: implementation of the Triangle Method (proposed by Zack, Rogers, Latt (1977), "Automatic measurement of sister chromatid exchange frequency", J. Histochem. Cytochem. 25 (7): 741–753) for automatic segmenting of grey level images.

11. Subdivide an image in blocks: to compute the coordinates of the Up Left Corner and Down Right Corner of the blocks (also overlapping), of size chosen by the user, in which the input image can be subdivided.