Photoshop CS3 Extended for BioMedical Research
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Applying a threshold to an image


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Photoshop CS3 Extended for BioMedical Research

with Eric Wexler

Video: Applying a threshold to an image

In this video, I am going to show a way to threshold an image and that's to simplify the image and get to a point that we can binarize it, have either a positive, which would be black in this case, or a negative which would be white. That way we can apply image analysis to it. What we see here is the picrosirius red-stained heart and what I want to do is to simplify the image so that we can easily move it in and measure the red using either Photoshop now or a different image analysis program.
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  1. 7m 56s
    1. Welcome
      2m 39s
    2. Disclaimer
      1m 44s
    3. Exercise files
      45s
    4. Understanding Photoshop CS3 Extended
      1m 41s
    5. Understanding which versions are covered
      1m 7s
  2. 20m 30s
    1. Understanding imaging in biomedical research
      5m 15s
    2. Understanding research image workflows
      4m 6s
    3. Understanding image fundamentals
      3m 29s
    4. Understanding image detection
      7m 40s
  3. 16m 47s
    1. Understanding digital images
      5m 28s
    2. Understanding image file types
      6m 33s
    3. Understanding objective imaging
      4m 46s
  4. 22m 1s
    1. Understanding the default workspace
      4m 0s
    2. Creating a custom workspace
      5m 31s
    3. Working with keyboard commands
      4m 20s
    4. Customizing preferences for research
      3m 50s
    5. Understanding the History Log
      4m 20s
  5. 18m 9s
    1. Learning to always work from a copy
      2m 23s
    2. Opening files in Photoshop
      4m 13s
    3. Introduction to Adobe Bridge 2.0
      2m 25s
    4. Using the Adobe Camera Raw Converter
      3m 34s
    5. Using the DICOM Importation interface
      4m 18s
    6. Working with scanned image sets
      1m 16s
  6. 13m 46s
    1. Organizing images
      5m 0s
    2. Applying rank, keywords, and filters
      6m 9s
    3. Working with image stacks
      2m 37s
  7. 27m 54s
    1. Understanding color modes
      4m 27s
    2. Understanding the Info panel
      7m 49s
    3. Reading the Histogram panel
      5m 48s
    4. Understanding color composition with channels
      6m 9s
    5. Comparing multiple images
      3m 41s
  8. 25m 19s
    1. Resizing images
      5m 0s
    2. Resizing the image canvas
      8m 11s
    3. Joining images with compositing
      7m 8s
    4. Using Auto Align and Auto Blend
      2m 5s
    5. Applying a threshold to an image
      2m 55s
  9. 23m 45s
    1. Considering adjustments
      2m 19s
    2. Understanding exposure controls
      1m 7s
    3. Optimizing exposure with Levels
      5m 1s
    4. Optimizing exposure using Curves
      7m 24s
    5. Removing color casts
      3m 3s
    6. Reducing chromatic aberrations
      4m 51s
  10. 25m 41s
    1. Understanding layers
      4m 21s
    2. Working with adjustment layers
      1m 35s
    3. Using layers to compare histological localization
      4m 41s
    4. Optimizing a fluorescent image
      4m 27s
    5. Creating a false-color image
      4m 25s
    6. Working with Smart Objects
      4m 13s
    7. Using selective desaturation
      1m 59s
  11. 1h 0m
    1. Understanding the Analysis menu
      3m 4s
    2. Creating a calibration
      3m 56s
    3. Selecting data points
      3m 0s
    4. Using the Marquee Selection tool to isolate an area of interest
      4m 18s
    5. Tracing a selection using the Lasso tool
      3m 31s
    6. Using the Polygonal Lasso tool
      6m 47s
    7. Using the Magnetic Lasso to create an area of interest
      4m 1s
    8. Working with the Quick Select tool
      4m 11s
    9. Using the Magic Wand
      4m 11s
    10. Creating a noncontiguous selection using the Magic Wand
      1m 54s
    11. Creating a selection using Color Range
      4m 32s
    12. Using the Selection tools for visual dissection
      2m 29s
    13. Using the Count tool
      5m 59s
    14. Using the ruler tool with calibration
      4m 28s
    15. Extracting data from the Measurement Log
      3m 41s
  12. 26m 31s
    1. Adding Scale bars manually
      4m 18s
    2. Adding Scale bars automatically
      5m 20s
    3. Adding text to images
      4m 50s
    4. Adding arrows to images
      6m 29s
    5. Adding vector shapes to images
      2m 57s
    6. Adding borders to images
      2m 37s
  13. 32m 29s
    1. Creating contact sheets
      4m 8s
    2. Combining images for presentation
      9m 35s
    3. Using the Bridge Slide Show feature
      2m 58s
    4. Creating a representative grayscale image
      6m 29s
    5. Using the Print interface
      2m 47s
    6. Integrating images into Microsoft Office files
      6m 32s
  14. 15m 23s
    1. Optimizing a DICOM image
      3m 49s
    2. Creating a DICOM animation
      7m 2s
    3. Annotating and optimizing animation
      4m 32s
  15. 1m 0s
    1. Goodbye
      1m 0s

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Watch the Online Video Course Photoshop CS3 Extended for BioMedical Research
5h 37m Intermediate Jan 25, 2008

Viewers: in countries Watching now:

Veteran pharmaceutical research scientist and member of Adobe's Biomedical Image Advisory Group, Eric J. Wexler shares his experience creating detailed biomedical imaging in Photoshop CS3 Extended for Biomedical Research. Eric shows how to use Photoshop CS3's selection, analysis, and editing tools to evaluate an image's color composition, modify images for research, optimize exposure with levels and curves, transform images with layers, and compensate for acquisition problems and limitations. Eric also explains how to add reference information to images, annotate and optimize DICOM animations, and share finished images with colleagues. Exercise files accompany the tutorials.

NOTE: Actual biological research images are used for this title's examples. Some of these images, including those of internal organs and dissected animals, may be considered graphic or offensive to some viewers. Viewer discretion is strongly advised.

Topics include:
  • Understanding imaging in biomedical research
  • Getting started in Photoshop
  • Organizing digital assets
  • Working with image stacks
  • Evaluating image color and histograms
  • Modifying images for research
  • Compensating for acquisition problems and limitations
  • Adding reference information to images
  • Sharing work
  • Optimizing and creating a DICOM image or animation
Subject:
Photography
Software:
Photoshop
Author:
Eric Wexler

Applying a threshold to an image

In this video, I am going to show a way to threshold an image and that's to simplify the image and get to a point that we can binarize it, have either a positive, which would be black in this case, or a negative which would be white. That way we can apply image analysis to it. What we see here is the picrosirius red-stained heart and what I want to do is to simplify the image so that we can easily move it in and measure the red using either Photoshop now or a different image analysis program.

First I am going to correct the image, I will bring up the Curves command with the Command or Ctrl, on the PC, +M and I am going to set a white point by clicking on Set White Point eyedropper and moving it to an area which has no tissue. Then we will hit OK and next, and I did show this previously, we are change the way we look at this image from RGB, and we're changing to the mode to CMYK. Then we did remember that magenta was the most appropriate single channel to look at just the pure intensity levels of the stains we are interested in. So what I can do is I can remove the other channels by right-clicking, Delete, right-click on yellow, Delete, and right- click on black and Delete. Now I have a channel with a single intensity.

Now we want to convert this to a gray scale image. So we go to Image > Mode > Grayscale and that converts the single intensity, removing the color of just what we can see, in this case the black matching the stain. To make this into a one-bit image, we need to threshold it and again we go to Image > Adjustments and down near the bottom is Threshold. Now in this case, we would be testing out different thresholds making sure that the most appropriate setting for analysis and that would be done by doing multiple experiments and testing this out on some sort of standards, a way to validate our method.

In this case, I am just going to move the threshold up to 146 and I will make sure that every subsequent image researched would the same settings so that they are comparable. We hit OK. Now I convert this directly into bitmap, Mode > Bitmap. The resolution of the original image is 300 and we want to keep that. In this case, we can go 50% threshold, hit OK and now we can analysis this sample knowing that the black represents the positive stain and the white is just tissue that has not been stained.

There is the one last item I wanted to show you about how Photoshop can be used to adjust images for additional work. In the next set of videos, I will be going over the concept of overcoming some of the acquisition limitations.

There are currently no FAQs about Photoshop CS3 Extended for BioMedical Research.

 
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