1. Photoshop / Illustrator Workshop
November 15th 2016
Alphonse Chu
alphonse.chu[at]yahoo.ca

2. Outline Digital Images File Formats Resolution – DPI
Publication Requirement
Working with images
Photoshop Basics
Composite images
Tools
Vector Graphics - Illustrator

3. Digital Images - Capturing

4. Digital Images – Image Sensor
The image sensor is a matrix of small sensors named pixels
Each pixel records the intensity of light
Once the intensity of light is recorded, a computer generates the image

5. Digital Images – Color Images
Color is separated into 3 basic colors (channels) with filters
Red
Green
Blue
Intensity of each channel is recorded
Each pixel combines the 3 channel to create a color image
Additive colors

6. Image Formats TIFF (Tagged Image File Format)
‘Raw’ or Lossless data format
Uncompressed image
Contains every bit of information (Data not discarded)
Used for publications
JPEG (Joint Photographic Experts Group)
‘Processed’ or Lossy data format
Compressed image
Contains only useful bits of information (Data is discarded)
Not used for publications

7. Image Formats Property TIFF JPEG Acronym Tagged Image File Format
Joint Photographic Experts Group
Type of Format
Raw or Lossless
Processed or Lossy
Compression No
Yes
Bit Information
Every bit of information saved
Only useful bits of information saved
Loss of information
No Data Loss
Some data is lost
Publication Use
Yes, but not all journals

8. Lossless vs Lossy (TIFF vs JPEG)
Downsampling

9. Resolution - DPI Resolution DPI and PPI Important for creating figures
Number of pixels in the Width and Height of the image
DPI and PPI
Important for scanning images and final figures
Dots Per Inch: Usually referred in Printing or Scanning
Pixels Per Inch: Usually referred in digital images

10. Publication Requirements
Figures
PowerPoint
EPS Format
Final DPI / PPI settings for the final figure
Make sure to check the journal requirements before submitting

11. Publication Requirements - Examples
PLOS One
Cell
File Format
TIFF or EPS
Dimensions
Width: 789 – 2250 pixels (at 300 dpi). Height maximum: 2625 pixels (at 300 dpi).
Resolution
300 – 600 dpi
File Size
<10 MB
Text Within Figures
Arial, Times, or Symbol font only in 8-12 point
File Format
TIFF or PDF
Dimensions
Max width & height 8 x 11 inches
Resolution
300 dpi (color figure)
500 dpi (black & white)
1000 dpi (line art figure)
File Size
<20 MB
Text Within Figures
Arial, Helvetica (no point size specified)
Genes & Development
Journal of Clinical Investigation
File Format
GIF, TIFF, EPS, or JPEG
Dimensions
N/A
Resolution
File Size
Text Within Figures
File Format
TIFF, EPS, PDF, AI
Dimensions
9-18 cm width
Resolution
600 ppi
File Size
N/A
Text Within Figures

12. Working with Images 1) Microscopes
Capturing from Instrument (Microscopes)
Every instrument and software combination is different
Use TIFF if possible
If available set highest dpi possible
Capture each channel individually if possible.
If the microscope software combines each channel, into a multipage TIFF you will have split them with IfranView Photoshop doesn’t do it.
Demo

13. Working with Images 2) Scanning Film
Import Directly into Photoshop
File
Import
WIA Support
Select your Scanner
Scanner software should launch
Capturing from Film
Scan in transparency mode
Use TIFF
If available set dpi or ppi to
Demo

14. Working with Images 3) Storage/Backups
As soon as the images are acquired, make a BACKUP COPY
DO NOT use the acquisition computer as a backup
Ideally the copy is on reliable/redundant storage (i.e. University Network Drives or Dropbox)
External hard drives are ok, but can fail (i.e. dropping it, accidents with liquids, etc)
ALWAYS work on COPIES of images
If something goes wrong, you can go back to the original

15. Composite Images Each fluorophore was captured in a different channel
Copy one of the images
Open in Photoshop a new file in RGB mode
Uses the dimensions of the copied image for the new file
Paste the copied image in the correct channel
Repeat for each channel/fluorophore
Adjust Levels for each channel (Don’t forget the ALT button)
Demo

16. Warning - Disclaimer
Photoshop is a powerful image processing tool, however, one should be careful with the adjustments, because one can change the result or the interpretation with image adjustments!
Demo

17. Useful Tools Rotating and Image Counting Straighten an image Cropping
Image  Image Rotation
Counting
Image  Analysis  Count Tool
You can rename the count groups with more descriptive names
To add a new count group click on the folder, give it a descriptive name and a new color
Straighten an image
Set up a crop box
Click on Straighten
Draw a straight line with a reference on an image
Cropping
Select crop tool and select the area you want to keep
Demo

18. Why Vector Graphics?
Enlarging an image with a set resolution causes pixelation
Each pixel is enlarged and causes the quality/sharpness of the image to decrease

19. Why Vector Graphics?

20. Vector Graphics
Vector graphics allows you to change the size of your text, shapes without loosing details
Basically a file that describes where each shape/text is located, the color etc. (Like a protocol)
If you increase or decrease the size, the shape/text is changed proportionally
%PDF-1.5
<</Metadata 2 0 R/OCProperties<</D<</ON[6 0 R 29 0 R 74 0 R R R R]/Order R/RBGroups[]>>/OCGs[6 0 R 29 0 R 74 0 R R R R]>>/Pages 3 0 R/Type/Catalog>>

21. Vector Graphics – Adobe Illustrator
Easy to use and intuitive
Make entire figures
Add excel graphs (some additional work required)
If you add images to the illustrator file (i.e. IF/Staining) don’t forget to embed them!
Resizing is easy!
Save as EPS (Standard Specification Format)for publication.
Demo

22. Adobe Suite & Open Source
Subscription base service
Discount available for students (Oct 28th exchange rate )
Annual Monthly payments
19.99 USD – CAD
Prepaid Yearly payments (No Savings if you prepay)
USD – CAD
Open Source Version of Photoshop
GIMP
Open Source Version of Illustrator
InkScape