ImageJ Resources

http://rsbweb.nih.gov/ij/
http://www.fmhs.auckland.ac.nz/sms/biru/facilities/analysis_resources.aspx

Learning ImageJ

ImageJ is a fantastic light-weight tool to analyze and manipulate images. I needed to use it for quickly analyzing microscopy images. Here I will list features of ImageJ that I found particularly useful for my purposes:
- I took a bunch of images at various gains to find out the point where bleaching starts occurring. So I have a series of images in which the pixel intensity varies from 0 to 255.

ImageJ allows me to load the images as a stack and calculate the maximum pixel value in each image by selecting the whole image and hitting 'm' (for measure). Plotting the maximum value gives this:

So, bleaching occurs somewhere between a gain of 450 and 475.

Batch processing images in Gimp

Over the past few weeks I've had to apply a specific set of changes to a large number of images. Doing this repeatedly took a great toll on my soul and Gimp came to my soul's rescue. Take a read at this and this and help yourself.

Joining images using ImageMagick's convert

convert +append list_of_figures out_1.png
convert +append list_of_figures out_2.png
convert +append list_of_figures out_3.png
convert -append out_1.png out_2.png out_3.png final_out.png

+append puts images side by side while -append adds them top down.
convert -border 2x2 in.png out.png
This puts a light border around images which comes in handy when creating a grid of images from a bunch of individual images which have no border.

Labeling figures

http://www.imagemagick.org/Usage/annotating/
This website offers a  nice way to add labels to images that "convert" can handle. I thought it was a nice idea to have my name on figures I generate.