Re: Saving high resolution networks

[Satish]

Hi,

I have made a network using cytoscape.

I want to save it as a graphic (Jpeg) with a resolution of 300 dpi or more.

I tried the cytoscape option of export > graphics and selected 300 DPI, but after i save it.. it shows only 96 dpi?

How could i create publication quality images (more than or eual to 300 dpi.)
Kindly help

--
Satish Balakrishnan
+91-992-0823777
Fred Allen  - "The last time I saw him he was walking down lover's lane holding his own hand."

[Maital Ashkenazi]

Hi Satish,

On Mon, May 4, 2009 at 12:02 PM, Satish <xsat...@gmail.com> wrote:

Hi,

I have made a network using cytoscape.

I want to save it as a graphic (Jpeg) with a resolution of 300 dpi or more.

I tried the cytoscape option of export > graphics and selected 300 DPI, but after i save it.. it shows only 96 dpi?

Which Cytoscape version are you using? There have been some changes in image export. You are encouraged to use the latest version (2.6.2).

How could i create publication quality images (more than or eual to 300 dpi.)

You could export the image in vector format, such as PDF or SVG.

Hope this helps,
Maital
 

[Vijayaraj Nagarajan]

Hi Satish,

You can generate excellent publication quality images in Cytoscape.

When you do EXPORT -> Network View As Graphic ->

after choosing JPEG as the format and after naming the file, when you get the "EXPORT BITMAP OPTIONS"....

Increase the ZOOM to 300% or 400%... or 500% or more...
and you will see the corresponding change in the height and width PIXELS.

You can then select the "Resolution" as 300 DPI...

This should give you a pretty high resolution image.

-Vijay
NIAID/NIH

[Satish]

Hi Vijayaraj,

I have done all that ... but after u save at 300 dpi, check the resolution in some image viewer softwares like microsfoft office picture manager. It says 96 DPI and not 300 DPI. I tried to upload for publishing with a manuscript and even they said its a low resolution image..

Hi mailtal,

I am using 2.6.2 only. i haven tried other formats. but since jpeg and BMP does not save in 300 dpi i doubt it will in pdf too atleast in my case. I have just used spring embedded layout.

--
Satish Balakrishnan
+91-992-0823777
Emo Philips  - "I got some new underwear the other day. Well, new to me."

[Vijayaraj Nagarajan]

Hi Satish,

When you export the image from Cytoscape.....

The ZOOM sets the pixel dimensions in Cytoscape.
The DPI sets the document size.
When you set the DPI in Cytoscape, you will see the document height and width changing....but the pixel dimensions remain same.

The resolution basically is all about the PIXEL dimensions. So if you can export your image from Cytoscape with high pixel dimension, you can always take that image and set the DPI in an image editor like photoshop or GIMP. I did that in GIMP and it works great for me.

The following link might help you get an idea about DPI and pixel dimensions....

http://blog.fotolia.com/us/faq/buyer/dpi-_digital_photography-_phot.html

Just to give you hope that you can definitely get excellent publication quality images from Cytoscape.... following is the link to one of my Cytoscape generated image published as a Supplemental figure in the Journal of Antimicro. Chemother.

http://jac.oxfordjournals.org/cgi/content/full/dkn363/DC1

Goodluk and have fun.

-Vijay
NIAID/NIH

[Karthik Raman]

Hi Satish,

I think it might be a good idea to export as PDF? That way you can get
a much better resolution. From PDF, you will be able to create a TIFF
or a JPG with whatever resolution your journal asks for...

Regards,
Karthik

On May 4, 6:36 pm, Vijayaraj Nagarajan <vir...@gmail.com> wrote:
> Hi Satish,
>
> You can generate excellent publication quality images in Cytoscape.
>
> When you do EXPORT -> Network View As Graphic ->
>
> after choosing JPEG as the format and after naming the file, when you get
> the "EXPORT BITMAP OPTIONS"....
>
> Increase the ZOOM to 300% or 400%... or 500% or more...
> and you will see the corresponding change in the height and width PIXELS.
>
> You can then select the "Resolution" as 300 DPI...
>
> This should give you a pretty high resolution image.
>
> -Vijay
> NIAID/NIH
>

> On Mon, May 4, 2009 at 5:02 AM, Satish <xsati...@gmail.com> wrote:
> > Hi,
>
> > I have made a network using cytoscape.
>
> > I want to save it as a graphic (Jpeg) with a resolution of 300 dpi or more.
>
> > I tried the cytoscape option of export > graphics and selected 300 DPI, but
> > after i save it.. it shows only 96 dpi?
>
> > How could i create publication quality images (more than or eual to 300
> > dpi.)
> > Kindly help
>
> > --
> > Satish Balakrishnan
> > +91-992-0823777

> > Fred Allen <http://www.brainyquote.com/quotes/authors/f/fred_allen.html> - "The last time I saw him he was walking down lover's lane holding his own
> > hand."
>
>

[Peng-Liang Wang]

I just did a test. This is a bug in the view export. The resolution parameter has no effect on the quality of exported image for jpeg, Bitmap.

 

But PDF and SVG format should be fine.

 

Peng

[Keiichiro Ono]

Hi.
I do not recommend to use export as jpeg image for publications. It
is mainly for web or other online documents. If you need to export an
image for papers/posters/books, you must use vector graphics, usually
PDF. In that case, you can create any DPI bitmap from that.

Kei

2009/5/4 Satish <xsat...@gmail.com>:

--
Keiichiro Ono ko...@ucsd.edu

Cytoscape Core Developer Team: http://www.cytoscape.org/
UCSD Bioengineering Ideker Lab: http://chianti.ucsd.edu/idekerlab/

[Satish]

Ok Guys..

Thank you ..

I will try the suggestions you guys mentioned and get back .. I guess saving it as PDF is one of the best option..


Thank you once again