links for home page    Imaging and Analysis in Microscopy...Tools and Consulting by Imaging Expert Gerald (Jerry) Sedgewick


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Cool science images from microscopes
  checkmark Learn at Your Own Pace
  checkmark Go Back to Where You Left Off
  checkmark Be Confident Your Staff is Trained
  checkmark Get Certificate for your CV from course instructor (Jerry Sedgewick, Author of "Scientific Imaging with Photoshop: Methods, Measurement and Output."
  checkmark Master Photoshop methods for Color Brightfield (Histological samples), Fluorescence and Grayscale (EM, Phase, DIC, etc.).
  checkmark Learn Proper Techniques: Correct images, do not Doctor them.
  checkmark Take Courses as you find time (on demand), and return to where you left off.
  checkmark Keep a Record of What you do in Post-Processing



  The Best Environment for Using Photoshop
View properly on computer screen, set-up Photoshop workspace, and learn which palettes should be open to get objective data and relevant information about your images.

Learn to Avoid Saving over Originals
Methods presented with steps included to avoid saving over original images.

Means to Record Steps Taken in Photoshop (Keep a Log)
In versions of Photoshop more recent than Photohop 7, log all steps used with a “history” log.

How to Rectify “Scientific” Image File Types
Remedy loss of visual information when 10-, 12-bit and 14-bit images are saved in a 16-bit “wrapper” leading to a black or dark image display in Photoshop; change indexed color images so that Photoshop functions can be used.

Steps for Creating a Photo-Montage from several images
“Stitch” together several adjacent high magnivication images to make a larger image (versions CS2 and more recent).

Method for Creating In-Focus Image from Several Images
Use Photoshop’s extended focus feature for creating an in-focus image from several images (Photoshop CS4 and more recent only).

Means for Increasing Dynamic Range
Learn how to increase the dynamic range for those images containing features that are overly bright with accompanying overly dark features (Photoshop CS2 and more recent versions).

How to Work with Movies and Image Stacks
Open AVI and MOV formatted movies in Photoshop CS3 and more recent versions. Image stacks can be saved in these formats, and then adjustments can be made to the whole stack when a movie file.

Z-Project Methods for Image Stacks
Min, Max, Mean, Range, Standard Deviation, Median, Sum, Entropy, Skewness and other statistical methods can be used to merge several images into one image, usually a “z-projection” in the world of confocal microscopy.

Image Rotation, Straightening, and Cropping
Rotate/Flip, Crop while retaining the entire image in case it is needed later, and crop more than one image to the same dimensions; align (straighten) images along a horizontal or vertical axis in 2 easy steps.

Methods for Correcting Uneven Illumination (Critical for Densitometry)
Correct for uneven illumination from a brighter center “spot” and darker edges (vignetting); and correct for other uneven patterns when having taken a flatfield image, or when using the image itself as the reverse image to correct; remove uneven pattern typical to DIC (Differential Interference Contrast) images, and to other images with large, uniform areas (e.g, TEM, Phase, Nomarski, etc.).

How to Correct for Noise
Correct for random noise, noise introduced by video devices (including confocal), color noise from chromatic aberration (color fringing), and for other contributions.

Tonal and Color Adjustments Made Objectively and By Numbers
Tonal adjustment to map image to its full dynamic range (manual and auto), tonal adjustments to target histograms to better show details (equalize), linear adjustments to match brightnesses of 2 or more images (for densitometry), histogram matching images for consitent contrast and color, using white eyedropper tool to color balance.

Visualization Techniques for Fluorescent Images: Co-Existence (colocalization), Merging, & Colorizing
Use method for semi-quantitative measurement and visualization of co-existence for monitoring initial results (scatterplots and other methods are best for publication), merge several channels to show several fluorophores in one image, and colorize grayscale images and blue-colored images so that these are more visible.

Methods for Pseudocoloring and for Reducing the Range of Colors or Grayscale Tones
Pseudocolor images, and then edit the colors to better show differences in tone in critical areas; and use methods to reduce the number of colors or tones to better visualize experimental results.

Scale Bar Creation and Calibration
Calibrate pixel to your unit of measurement by the lens magnification used; insert scale bar with text.

Methods for Setting Resolution so that Images are Not Compromised
Re-set pixel resolution for output to posters, publication, Powerpoint, Word, and Acrobat.

Means for Sharpening Images to Reveal Hidden Details
Sharpen images according to 1 of 2 methods. Save the sharpened image to a layer so that it can be removed for publications that prohibit sharpening. Use techniques that help prevent over-sharpening.

Function for Applying the Same Corrections to Related Images
Use the Actions functions to create macros so that all corrections applied to 1 image can be applied to related images, including the controls. Include interactive steps and comments as reminders.

  Course Overview and Who The Course is For


Overview. This course shows proper methods for working with images taken in microscopy. Microscopy images have unique attributes not found in typical subject matter in photography; and the adjustments in post-processing are limited to those commonly accepted in the scientific community. The emphasis in these courses is to avoid any adjustment that would obscure details; and, conversely, to make adjustments to reveal visual details. Methods lead to “corrections” and not to “doctoring” or “enhancing.”

Furthermore, objective means are shown with tools built into Photoshop, when possible, to determine extent of corrections.

Photoshop Versions. These course instruct in versions of Photoshop from 6 to 13 (CS6). More functions are available in so-called “Extended” versions from 10 (CS3) to 13, and for these it is especially important to take the course.

Approach. These courses use Powerpoint slides, a provided manual as a reference, and videos with labeling as an aid to those who use English as a 2nd language (and the rest of us). Videos do not require audio accompaniment.

Certificate. To obtain a certificate for your CV, provided images will need to be corrected and then emailed to the course creator (Jerry Sedgewick). After review, you will receive a certificate upon approval. At any time during the course, you can email Jerry to get help.

Student Backgrounds. These 4 courses are for researchers, editors, principal investigators, reviewers, students and staff members from beginner to advanced levels. You must have a basic knowledge of running a computer: with the ability to create file folders, find the file folders, and then open files from folders (versus double clicking on the image files and expecting them to open in Photoshop)

Time Investment. The Post-Processing courses will take 15 - 20 hours, depending upon the course, level of experience and version of Photoshop (more recent versions contain more functions that are presented).


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