Schedule:
2/15: Photoshop - colorizing microscope images using channels
3/1: Photoshop - making ChIP-chip graphs from SignalMap files
3/8: Photoshop - colorizing staining images
3/15: Illustrator - creating bar graphs
3/22: Illustrator - converting Excel graphs (scatterplots, etc.)
3/29: Photoshop & Illustrator - building complexes using shapes
Links:
Download the Photoshop trial version:
https://www.adobe.com/cfusion/tdrc/index.cfm?product=photoshop&promoid=GYSGB
Download the Illustrator trial version:
https://www.adobe.com/cfusion/tdrc/index.cfm?product=illustrator&promoid=GXWGF
Download GIMP:
http://www.gimp.org/
Download Inkscape:
http://inkscape.org/
2/15: Photoshop - colorizing microscope images using channels
In this lesson we'll use the channels window in Photoshop to create merged microscope images. Prepare for this workshop by making sure you're familiar with the concept of channels and layers, by downloading the image files we'll be using from the links below, and by looking over the steps in the handout, also provided with a link below. If you have questions, please talk to me in advance, borrow a book or use the help files in Photoshop. (When you click on these image files, they'll come up in this page. Right-click on each one and choose "Save Image As" and save it to the location of your choice. You'll have to hit the back arrow to get back to this page.)
Image files to download: dapi.png, array.png, dpy27.png and merge.png
Step-by-step instructions:
workshop 1.pdf (revised on 2/15)
3/1: Photoshop - making ChIP-chip graphs from SignalMap files
In this session we'll use Photoshop to cut up, size, and colorize the ChIP-chip files generated by the SignalMap program on the PC in the computer lab.
Prepare for this workshop by making sure you're familiar with the layers window and the Photoshop toolbar. It would also be a good idea to try out the Nimblegen SignalMap program so you have at least a basic idea of how data is displayed there and what the options are. You'll need to download the image files we'll be using from the links below, and look over the steps in the handout, also provided with a link below. If you have questions, please talk to me in advance, borrow a book or use the help files in Photoshop. (When you click on these image files, they'll come up in this page. Right-click on each one and choose "Save Image As" and save it to the location of your choice. You'll have to hit the back arrow to get back to this page.)
Image files to download: NG data.png, final.png (You will also need a Photoshop template for this lesson, which I can't include here. I'll email it to everyone.)
Step-by-step instructions: workshop 2.pdf (revised on 3/1)
3/8: Photoshop - colorizing staining images
In this final Photoshop lesson we'll use the channels window again to colorize staining on a grayscale image. This will be fairly similar to what we did in the 2/15 session, so those of you who attended may be able to do it with just the handout, or feel free to join us for a review.
Prepare for this workshop by making sure you're familiar with the concept of channels and layers, by downloading the image files we'll be using from the links below, and by looking over the steps in the handout, also provided with a link below. If you have questions, please talk to me in advance, borrow a book or use the help files in Photoshop. (When you click on these image files, they'll come up in this page. Right-click on each one and choose "Save Image As" and save it to the location of your choice. You'll have to hit the back arrow to get back to this page.) We'll be using the images from Bobby's paper for this lesson, but I'm including the images from Andrew's paper as well because they were created in a similar but slightly different way. If there's time I'll go over that difference.
Image files to download: Bobbyexbw.png, Bobbyexblue.png, Bobbyexdone.png, Andrewexbw1.png, Andrewexbw2.png, Andrewexgreen.png, Andrewexdone.png
Step-by-step instructions: workshop 3.pdf
3/15: Illustrator - creating bar graphs
In this session we'll use Illustrator to create/adjust bar graph templates that can be used repeatedly for slides or figures.
Prepare for this workshop by making sure you're familiar with the basic tools in Illustrator. Obviously you'll also need to install the trial version if you don't have it. If you have general questions about using this program, please talk to me in advance, borrow a book or use the help files in Illustrator.
Image files to download: I sent this template to everyone via email.
Step-by-step instructions: workshop 4.pdf
3/22: Illustrator - converting Excel graphs (scatterplots, etc.)
In this session we'll use Illustrator to create charts in Illustrator using data generated in Excel. Again we'll use a template that can be remade repeatedly for slides or figures.
Prepare for this workshop by making sure you're familiar with the basic tools in Illustrator. Obviously you'll also need to install the trial version if you don't have it. If you have general questions about using this program, please talk to me in advance, borrow a book or use the help files in Illustrator.
Note: For this lesson you'll need to be able to save an Excel chart as a pdf file. It is unclear to me whether that requires Adobe Acrobat. I would suggest opening the data.xls file I sent via email to test this out in advance. Once you open the file (choose "ignore links" when prompted), click on the chart and choose File/Save As. If PDF is one of the options in the dropdown menu, you're good. If not, you probably need to install a trial version of Adobe Acrobat Professional as well (Not Adobe Acrobat Reader).
Image files to download: I sent the template.ai and data.xls files to everyone via email.
Step-by-step instructions: workshop 5.pdf (Revised on 3/24)
Examples of the various types of graphs this technique can be used for are provided below.
3/29: Illustrator and Photoshop - building complexes using shapes/Making compressed PDFs for journal submission
In this session we'll try to cover anything that's left.
There was a specific question about drawing complexes like the one pictured below. I'll go over the way I would do this in both Illustrator and Photoshop. I'm not going to make directions for this because it really depends on what you want.
I'l also go over how to make a compressed PDF for a journal submission. There is an instruction sheet for this process linked below.
If there's anything else you want you want me to demonstrate we'll do that at the end, so bring your questions.
Reminders from our discussion on drawing: workshop 6.pdf
Step-by-step instructions for compressing pdfs: PDF directions.pdf
Example complex:
