Spring 2008 Writing Workshops - PowerPoint PPT Presentation

Loading...

PPT – Spring 2008 Writing Workshops PowerPoint presentation | free to view - id: 4b295c-MzUzZ



Loading


The Adobe Flash plugin is needed to view this content

Get the plugin now

View by Category
About This Presentation
Title:

Spring 2008 Writing Workshops

Description:

Spring 2008 Writing Workshops Your Writing Project: Use OF Illustrations & Data Displays (CE) Mike Werle, Ph.D., Associate Professor, Anatomy & Cell Biology, KU SOM – PowerPoint PPT presentation

Number of Views:107
Avg rating:3.0/5.0
Slides: 45
Provided by: Michael2045
Category:

less

Write a Comment
User Comments (0)
Transcript and Presenter's Notes

Title: Spring 2008 Writing Workshops


1
Spring 2008Writing Workshops
  • Your Writing Project Use OF Illustrations Data
    Displays (CE)
  • Mike Werle, Ph.D., Associate Professor, Anatomy
    Cell Biology, KU SOM

2
Outline
  • What are common problems associated with
    publishing graphs?
  • Possible causes of these problems.
  • Possible solutions for these problems.
  • Examples of good graphing principles.
  • Use of images and color.

3
Survey of Scientific Editorsn25
  • Eileen K. Schofield, 2002, Quality of Graphs in
    Scientific Journals An Exploratory Study.
    Science Editor 2539-41.
  • Is quality of graphs a criterion for acceptance
    of manuscripts by your journal?
  • 16 Yes
  • 9 No

4
Schofield, 2002continued
  • Do your instructions to authors include details
    about preparation of graphs?
  • 18 Yes
  • 7 No
  • How do you handle poor-quality graphs?
  • 22 Return them to authors with instructions
  • 7 Make Corrections in your office
  • 2 Publish them without corrections

5
Top 10 ListSchofield, 2002
  • Too many patterns on bars
  • Use of both different symbols and different lines
  • Too many shades of gray on bars
  • Lines too thin (or thick)
  • Use of three-dimensional bars for only two
    variables
  • Lettering too small and font difficult to read
  • Symbols too small or difficult to distinguish
  • Redundant title printed on graph
  • Use of grey symbols or lines
  • Key outside the graph

6
What are possible causes of these problems?
  • Lack of clear and consistent instructions to
    authors???

7
Example 1Nature
  • Review version medium .jpg
  • Acceptable jpg, tif, gif,eps,ppt
  • Prefer 300 dpi.
  • Most referees view them on a monitor set to
    256 colours
  • sometimes they are only saved at 72dpi, whereas
    we recommend that 150 dpi is advisable
  • Please note that if your manuscript is accepted
    for publication, you will be asked to mail a disk
    and hard copy printout of the final versionWe
    cannot accept manuscripts formatted in MS Word
    2007

8
Example 2Journal of Neuroscience
  • 1, 1.5 or 2 column (8.5 up to 11.6 cm)
  • Color or grayscale 300 dpi
  • Halftone and line art 600 dpi
  • Bitmap and monochrome 1200 dpi
  • TIFF and EPS are only acceptable formats

9
Example 3Developmental Neurobiology
  • Go to RapidInspector at http//rapidinspector.cadm
    us.com/zwi/index.jsp
  • Once there you can submit your file and see if it
    is ok.
  • Only specs listed are 300 dpi in a CMYK color
    space for images.

10
I give up, lets go retro
  • Or can the computer save us??

11
Software
  • Ubiquitous, Low resolution output, limited
    control of formating. Cheap.
  • Steep learning curve, Expensive (499 academic
    version www.systat.com)
  • Pixel based, Industry standard, best for final
    touches at final resolution. (www.adobe.com
    Pricey 500-700)
  • Vector based, most flexible to change sizes, and
    resolutions (www.deneba.com about 400).
  • Microsoft Excel
  • SigmaPlot
  • Photoshop
  • Canvas

12
Softwarecontinued
  • Easy to learn and use. Limited output options
    (www.synergy.com) relatively cheap (140).
  • No WYSIWYG, steep learning curve (expensive).
  • KaleidaGraph
  • SAS
  • Others?

13
My Favorite Graph Protocol
  • Use Excel for data entry and statistics
  • Use Excel for graph rough drafts
  • Export graph (tiff or pict)
  • Redraw graph using Canvas (aka TRACE)
  • Since Canvas is vector based the graph can be
    easily and accurately resized.
  • Render file at correct size and dpi for the
    journal.
  • Repeat as needed

14
Move toward paperless review and publication
  • Computer screens are RGB.
  • Light is emitted from the screen.
  • Print version is usually CMYK
  • Light is reflected off the paper.
  • Composing the graph on your computer has many
    advantages, but

15
WYSIWYGBNWTRS
16
Monitor to Monitor Variations
  • Pixel density
  • Color depth
  • Gamma

17
Resolution
18
Resolution
19
Dithering
20
Outstanding Definitions
  • http//rapidinspector.cadmus.com/RapidInspector/do
    cs/index.html

21
Ideas for Better Graphs
22
Excellent TextbookThe Visual Display of
Quantitative Information, 2nd edition
(Hardcover)by Edward R. Tufte(32.80 _at_
Amazon.com)
23
Why Graphs?
  • Clearly show the details and patterns in your
    data.
  • Images show relationships between data points.
  • Words are best for abstract concepts.

24
Some Guidelines
  • The golden rectangle
  • Aim for around 1 unit tall by 1.6 units wide
  • Ink to information ratio
  • Dont have a lot of empty space
  • Make it easy for the casual reader
  • Horizontal format
  • Size should be dictated by the data

25
More Guidelines
  • 10 of the population is Red/Green color blind.
    Avoid using these as contrasts.
  • Do not use a colored background.
  • Keep is simple, no more than 7 /- 2 groups in a
    graph.
  • Do not use 3D effects.

26
From Visualizing Data, Raymond R. Balise,
Ph.D., Stanford University.
27
Top 10 ListSchofield, 2002
  • Too many patterns on bars
  • Use of both different symbols and different lines
  • Too many shades of gray on bars
  • Lines too thin (or thick)
  • Use of three-dimensional bars for only two
    variables
  • Lettering too small and font difficult to read
  • Symbols too small or difficult to distinguish
  • Redundant title printed on graph
  • Use of grey symbols or lines
  • Key outside the graph

28
The Good
29
(No Transcript)
30
(a,b) Whole mounts of diaphragm muscles from
wild-type (a) and Musk-H (b) P0 mice were stained
with Alexa594alpha-BGT (red) and antibodies to
Neurofilament and Synaptophysin (green).
Anatomically matched areas from the left
hemi-diaphragm were imaged from the medial to the
costal edge of the muscle. In wild-type mice,
synapses form only in the central region,
adjacent to the main intramuscular nerve (a). In
Musk-H mice, synapses are distributed throughout
the whole muscle (b). (c) Images of synapses in
wild-type mice and in the central and peripheral
regions of muscle from Musk-H mice show that the
general structure of ectopic synapses in Musk-H
mice is normal. (d) In wild-type mice, synapses
were concentrated in a narrow central band that
covers 510 of the muscle, whereas in Musk-H
muscle synapses are distributed throughout
(approx90) the muscle (mean plusminus s.e.m., n
3 mice for each genotype). (e) The number of
muscle fibers was similar in Musk-H and wild-type
mice (see Supplementary Fig. 2). (f) The number
of motor neurons was normal in Musk-H mice (see
Supplementary Fig. 3). (gi) Terminal sprouting
was not observed in muscle from wild-type P11
mice (g) and observed only rarely (4/495
synapses) in diaphragm muscles from Musk-H mice
(n 3 i). Scale bar, 200 mum (a,b,f) 10 mum
(c,gi) 100 mum (f).
31
Overall ratio 1 to 1.44Graph 1 to 1.6
32
The Scary
33
Barcharts are great for trends
34
Should there be a blue bar on the right hand
side??
35
The Bad
36
  • Figure 5. The width of the central band of AChR
    clusters in diaphragms at E14.5 is narrower in
    agrn/ (A) than in control (A') littermates. A
    difference is also found between Hb9/ mutants
    (B) and control (B') littermates. C, Widths of
    AChR cluster bands (means SE) in agrn/ and
    Hb9/ mutants relative to control littermates.
    Data are based on five agrn/ mutants (2
    litters p lt 0.05) and four Hb9/ mutants (3
    litters p lt 0.1). Scale bar, 70 µm.

37
Figure 2. Reduction in transgene expression after
Dox withdrawal. The CAErbB2 transgene has an
internal ribosomal entry sequence and a firefly
luciferase open reading frame cloned in-frame
downstream. Thus, from one mRNA, two proteins,
CAErbB2 and luciferase, are translated. Hence,
luciferase activity was used as surrogate for
CAErbB2 expression. Diaphragm muscle extracts
were used to measure luciferase activity. At
E15.5, when Dox-food was removed, average
luciferase activity is high in extracts from BT
diaphragm. By E17.5, average luciferase activity
is reduced nearly 100-fold. By birth, average
luciferase activity is reduced to levels in ST
controls. Results are presented as mean SD.
38
The Ugly
39
  • Violates almost every rule

40
Images
  • You can never never never have too many pixels.
  • Use Photoshop to enhance contrast, brightness and
    colorize.
  • Add labels and scale bars as layers, you can
    change these easily.
  • Use Photoshop to reduce the image as needed.
  • Keep the original for future adjustments

41
Figure 1. Electron micrograph of a neuromuscular
junction from a mouse diaphragm. The left panel
is an electron micrograph of a normal mouse
neuromuscular junction. The right panel is the
same image with the structures colorized and
labeled. There are two muscle cells in red or
light red. The muscle cell on the bottom is the
cell that is innervated by the nerve terminal.
The nerve terminal is green, and labeled NT.
There is a separate muscle cell that sits on top
of the nerve terminal. The terminal Schwann cell
is colored yellow, and is labeled SC. The sub
synaptic nucleus of the muscle cell is dark red,
and labeled N. The mitochondria in the muscles
and nerve terminal are colored blue. Within the
nerve terminal are clusters of synaptic vesicles
(dark green). These synaptic vesicles are
focused on the active zones which are dark black.
The active zones are found opposite the mouths
of the junctional folds (JF). The synaptic basal
lamina (SBl) is found in the unlabeled area
between the nerve terminal (green) and the Muscle
Cell on the bottom.
42
(No Transcript)
43
(No Transcript)
44
Outline
  • What are common problems associated with
    publishing graphs?
  • Possible causes of these problems.
  • Possible solutions for these problems.
  • Examples of good graphing principles.
  • Use of images and color.
About PowerShow.com