Image Control: Responsible Digital Data Processing - University of ...

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15 Νοε 2013 (πριν από 3 χρόνια και 11 μήνες)

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Image Control:


Responsible Digital Data Processing

Diana Lim

University of Utah Molecular Medicine Program

Workflow

Data
Collation

Photoshop

Illustrator

Proofing

Archiving

2

Data
Collation

Photoshop

Illustrator

Proofing

Archiving



Drafting your story


Collect digital data
into folders


Sketch figures in
PPT, or hand draw

3

Data
Collation

Photoshop

Illustrator

Proofing

Archiving


Adjust exposure


Crop Images

4

Data
Collation

Photoshop

Illustrator

Proofing

Archiving


Organize panels,

l
abeling


Output to final formats

5

Data
Collation

Photoshop

Illustrator

Proofing

Archiving


Verify against original data


Check production quality


6

Data
Collation

Photoshop

Illustrator

Proofing

Archiving


Electronic Lab
Notebook stored
for long
-
term
retrieval

7

Data
Collation

Photoshop

Illustrator

Proofing

Archiving



Drafting your story


Collect digital data
into folders


Sketch figures in
PPT, or hand draw

8

Your Data Mountain

Focused down to four pages

9

Collating Data


Collect digital data into
folders on the server


Naming files: Fig#_Descriptor_081413.app


Sketch
figures in PPT, or hand draw


10

Data
Collation

Photoshop

Illustrator

Proofing

Archiving


R
epresentative image


Crop Images

11

Representative Image
I
s True to Reality

12

Rossner M
,
Yamada KM
. What's in a picture? The temptation of image manipulation.
J
Cell Biol.

2004 Jul 5;166(1):11
-
5.

Choosing Representative Images

Of your replicate experiments,

the representative image is not necessarily

the Best image

13

Loading Controls

14

Rossner M
,
Yamada KM
. What's in a picture? The temptation of image manipulation.
J
Cell Biol.

2004 Jul 5;166(1):11
-
5.

Adding/Deleting Isolated Data

15

Rossner M
,
Yamada KM
. What's in a picture? The temptation of image manipulation.
J
Cell Biol.

2004 Jul 5;166(1):11
-
5.

Always Leave a Distinctive Line

To Display Image Modifications


Always display white or black line to indicate deleted
lanes in blots, sequence, or other data


Holding the shift key down while sliding image across
prevents vertical displacement of bands


Inset boxes can be used e.g. for zoom in/zoom out in
microscopy, but must clearly display box around any
data inserted into an original image.


Holding the shift key down while sliding diagonally
prevents distortion of the image



16

Exposure Adjustment of Isolated Data

17

Rossner M
,
Yamada KM
. What's in a picture? The temptation of image manipulation.
J
Cell Biol.

2004 Jul 5;166(1):11
-
5.

Microscopy Images

Exposure and Blending Channels


All panels must be treated exactly the same.


Saving levels in your electronic lab notebook is important
so you can reapply them

18

Collated From Original TIFs

19

Color Channels and Scale Bars

20

Older Method of Saving Levels

21

Cropping Brings Us Closer

to the Main Characters

22

Our Current Work
-
In
-
Progress

23

Revealing Repositioned Cell Images

24

Rossner M
,
Yamada KM
. What's in a picture? The temptation of image manipulation.
J
Cell Biol.

2004 Jul 5;166(1):11
-
5.

Ansel

Adams

Moonrise, Hernandez, New Mexico, 1941



Massaging images has been around for a long time


Artistic interpretation is
a

strength of Photoshop but is
not appropriate for scientific image processing

25

Data
Collation

Photoshop

Illustrator

Proofing

Archiving


Verify against original data


Check production quality


All authors and I can help
you

26

Look For These During Proofing


Symbol font, and other fonts, vary computer to
computer


Image flips

(PowerPoint)


Inverted colors in
grayscale

blots can make your
western look like a PCR

(Acrobat)


Color shifts from screen to print:


Check greens, blues, magentas


sepia toned
grayscales


27

Data
Collation

Photoshop

Illustrator

Proofing

Archiving


Electronic Lab
Notebook stored
for long
-
term
retrieval

28

Data Archiving


Use the server as your working Electronic Lab
Notebook then transfer for permanent storage


Long
-
term storage
unit/policies vary among
labs


CDs/DVDs filed with the white paper


e
-
mail attachments are terrible for long
-
term tracking of
the data files. BUT wise keep the conversation without the
attachments.

29

Data Archiving


Organize files for quick retrieval


Fig # is short, but better is your descriptor


Always include the date in your file name, servers can
corrupt the date saved


Quick response to an editor increases your honesty score

30

Example of Original Data Received for
Processing

31

Example of a Finished Data Folder


32

References


Rossner M, Yamada KM
.
What's in a picture? The temptation of image
manipulation.
J Cell Biol. 2004 Jul 5;166(1):11
-
5.


Gilbert N,
Science journals crack down on image manipulation
, Nature,
doi:10.1038/news.2009.991


Cromey

DW,
Twisted Pixels: ethical guidelines for the appropriate use and
manipulation of scientific digital images
.
Sci

Eng

Ethics.

2010 Dec;16(4):639
-
67.
doi
: 10.1007/s11948
-
010
-
9201
-
y.


Cromey DW.
Digital images are data: and should be treated as such.

Methods
Mol Biol. 2013;931:1
-
27.
doi
: 10.1007/978
-
1
-
62703
-
056
-
4_1.


Rossner

M,
How to Guard Against Image Fraud
. The Scientist Magazine 2006;


Editorial,
Gel slicing and dicing: a recipe for disaster
. Nature Cell Biology 2004:
275

33

Acknowledgements

Dean Li

Guy Zimmerman

Andy
Weyrich

Mary
Beckerle

Steve Prescott


Julia
Pili

Alex Greer

Linn Steele

Tatia

Forsgren


Computer Support

Rick Haycock

Jennifer Camp

Harold Nez

Ryan
Haver

Elliot Francis


Betty
Leibold

Students, Faculty, Post
-
docs,
Research Wizards



Reputation Reflects on All of Us

Non
-
scientific
Community

35

Summary


You are Ultimately Responsible for Data Integrity


Always be prepared to be audited. Your filing system
can help you.


Speedy response speaks to your honesty

36