Parte I. Introducción a ImageJ Parte II – Operaciones sobre píxeles Parte III - Filtros Parte IV - Análisis de imágenes

Parte I. Introducción a ImageJ Parte II – Operaciones sobre píxeles Parte III - Filtros Parte IV - Análisis de imágenes

Spots.tiff: Image courtesy of Wu Yuhong: 1. It is RGB 2. Low contrast 3. Uneven background (stripes from a scanner) 4. Size is given as 1.54x1.18 inches

The goal is to count, and measure the spots. The approach has to evolve, but here are the essential elements: 1. Since all of the spots appear to be black, color is not

significant, and one can use a monochrome image. 2. The background must be dealt with. 3. The spots need to be discriminated from the

background –several options. 4. We can scan a line across the image, storing the

coordinates.

Note the slight rise upwards, Also the range, from 140-ish to 130 or so for the largest dot.

Adjust contrast and brightness according to the histogram

Separate channels

red

green

blue

It appears that the greatest difference between the background and the signal is in the red channel, but there are stripes on the image.

Scan each channel.

red

green

blue

It appears that the greatest difference between the background and the signal is in the red channel, but there are stripes on the image.

Red channel

We make a rough determination of the threshold.

Exclude very small objects by selecting a size > 10

La transformada de Fourier se puede usar, entre otras cosas, para eliminar ruido periódico. También para realizar filtrados de suavizado o de realce.

La transformada de Fourier se puede usar, entre otras cosas, para eliminar ruido periódico. También para realizar filtrados de suavizado o de realce. http://imagej.nih.gov/ij/docs/guide/146-29.html#toc-Subsection-29.10

Bandpass Filter to smooth background

FFT Filtering

Here is one of the nifty

things you may use fft

filtering for. The laser

scanning confocal

microscope scans along

the X axis. If there is

noise in the laser, then

this shows up most

dramatically in adjacent X

axis scans. Filtering the

frequency of the

alternating X axis

intensities cleans up the

image.

FFT filtering example

Recursos usados para la elaboración de estas diapositivas:

» ImageJ, A Useful Tool for Image Processing and Analysis Joel B. Sheffield, Temple University.

http://rsbweb.nih.gov/ij/docs/examples/IJ-M&M08.ppt

» MRI ImageJ Workshop. Exercises 4 with solutions

http://dev.mri.cnrs.fr/wiki/imagej-workshop

» http://rsb.info.nih.gov/ij/docs/examples/FFT/index.html

» Operaciones morfológicas binarias

» Operaciones morfológicas binarias

» Operaciones morfológicas binarias

Original erosión

apertura= erosión+dilatación

clausura= dilatación+erosión

dilatación

Ejercicio Usa todo lo aprendido sobre Image J para intentar segmentar la imagen de células de músculo humano.

Consulta los trabajos en https://opera.eii.us.es/pid