Image analysis software

Dapple is the image analysis software used for adaptive circle segmentation. It performs the analysis by estimating the circle diameter for each spot. By taking the second derivative of the pixel intensity vs coordinate graph, the edges of the spots can be... 

Two important morphological parameters characterizing ball-milled powders are the particle and grain size of constituent phases within the powders. In our laboratory, the size measurement of the powder particles is carried out by attaching loose powder to sticky carbon tape and taking pictures under secondary electron (SE) mode in the SEM. The images are then analyzed by an image analysis software. The size of the powders is calculated as the particle equivalent circle diameter, ECD = AA/nf, where A represents the projected particle area. Usually from -300 to 700 particles are analyzed for each batch. 

Another expensive factor of HCS is software. All HCS instruments have on board tools for image analysis and various level of sophistication for data analysis and viewing. Often image and data analysis is done after the acquisition of the screening plates in order not to slow down the microscope. Vendors therefore offer off-line licenses increasing the cost of software further. The image analysis software installed on instruments is often restricted in functionality to deliver easy-to-use software, although some vendors... 

Carpenter A, Jones T, Lamprecht M et al (2006) Cell Profiler image analysis software for identifying and quantifying cell phenotypes. Genome Biol 7 R100... 

Kamentsky L, Jones TR, Fraser A et al (2011) Improved structure, function and compatibility for CellProfiler modular high-throughput image analysis software. Bioinformatics 27 1179-1180... 

Fig. 1. Schematic overview of the tumor spheroid-based migration assay. Tumor spheroids (TS) are transferred from their cuiture vessei or piate into a 96-weii fiat-bottomed migration piate pre-coated with an extraceiiuiar matrix (ECM) protein of choice (in this case, geiatin). Digital images of the spheroids are then captured at t=0 and once every 24 h for a period of up to 72 h, exemplified here by CAL spheroids. Image analysis software is used to calculate the spheroid size and extent of migration. Scale bar=100 p.m.

Import graticule images into the image analysis software to perform image calibration (see Note 18). This step is required for the first time only. For subsequent image analysis, simply select the required calibration settings. 

Import the migration assay images into the image analysis software and select the calibration settings depending on the microscope objective (lOx or 4x) used to obtain the images. 

Image calibration is required in order to obtain accurate measurements. The objective used (lOx or 4x) the units (pm) and the graticule measurements need to be entered into the image analysis software to obtain the correct calibration for the system used. 

Fig. 4. Application of bioinformatics tools to 2D-DIGE data analysis. Proteome data consisting of the normalized spot intensity values are exported from the image analysis software and their correlation with clinicopathological data examined. Using informatics tools including clustering algorithms and machine-learning methods, a novel cancer classification based on proteome data is established, and key proteomic features and proteins corresponding to biomarker candidates are identified.

The intimate contact data shown in Figure 7.16 were obtained from three-ply, APC-2, [0°/90o/0o]7- cross-ply laminates that were compression molded in a 76.2 mm (3 in.) square steel mold. The degree of intimate contact of the ply interfaces was measured using scanning acoustic microscopy and image analysis software (Section 7.4). The surface characterization parameters for APC-2 Batch II prepreg in Table 7.2 and the zero-shear-rate viscosity for PEEK resin were input into the intimate contact model for the cross-ply interface. Additional details of the experimental procedures and the viscosity data for PEEK resin are given in Reference 22. 

Quantitative analysis of these images is accomplished in the same manner as for any microscope image, depending on the detail of analysis desired. Automated image analysis software can be used to provide a variety of information. Crystal phase volume (solid fat content UNIT D3.i) can be obtained by counting dark pixels (according to some empirical threshold factor). 

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