ImageMagick

convert

• convert -list configure - list configuration for your install
• Overview
• -flip - horizontal mirror
• -flop - vertical mirror
• -crop XxY+Xoffset+Yoffset
• convert -delay 25 -loop 0 *.gif animation.gif - create an animated gif
• Take the biggest internal square - convert Christopher_Coletta_headshot.jpg -set option:size '%[fx:min(w,h)]x%[fx:min(w,h)]' xc:none +swap -gravity center -composite me_headshot_square.png
• Tile images- for i in *; do BASENAME=`basename $i _E.tif`; convert $i -crop 208x231 +repage ~/img/lymphoma-auto-color-tiled5x6/eosin/CLL/${BASENAME}_t%02d_E.tif; done
• +repage resets the coordinate system of an image to 0,0 being in the upper left. "completely remove/reset the virtual canvas meta-data from the images"
• -shave 2x0 - shave 4 total pixels from the width, 2 from left, 2 from right, and shave 0 pixels from top and bottom

identify

• full options
• also identify -verbose