Download ImageJ Cheat Sheet: Commands and User Interfaces and more Cheat Sheet Computer Applications in PDF only on Docsity!
Robert Haase (Myers lab, MPI-CBG); Benoit Lombardot, Noreen Walker and Gayathri Nadar (Scientific Computing Facility, MPI-CBG); Jens Ehrig (CMCB, TU Dresden)
Cheat sheet
ImageJ macro commands and user interfaces
Operator Description Example all yield a = 9
= Assignment a = 9 ;
+ Addition a = 3 + 6 ;
* Multiplication a = 2 * 4.5;
/ Division a = 27 / 3 ;
++ Increment by 1 a = 8 ; a++;
-- Decrement by 1 a = 10 ; a--;
+= Addition assignment a = 3 ; a += 6 ;
- = Subtraction assignment a = 11 ; a - = 2 ;
*= Multiplication assignment a = 2 ; a *= 4.5;
/= Division assignment a = 27 ; a /= 3 ;
Math command Description Example all yield a = 9
pow(x, y) x to the power^ of y^ a = pow( 3 , 2 );
sqrt(x) square root of x^ a = sqrt( 81 );
abs(x) absolute value of x^ a = abs(- 9 );
round(x) rounding of x^ a = round(9.4);
floor(x) rounding down^ of x^ a = floor(9.8);
String manipulation commands
output = replace(input, pattern, subst);
replace any occurrence of pattern in input by rsubst
outputArray = split(input, separator);
cut a string into a list of strings (array) according to the separator position(s)
length = lengthOf(string);
returns number of characters of the string (see below for “lengthOf(array)”)
result = startsWith(input, pattern);
returns true, if input starts with given pattern
result = endsWith(input, pattern);
returns true, if input end with pattern
// comments for code documentation
numericVariable = 5 ;
stringVariable = "text value";
builtInCommand();
Macro language elements
a = 5 ;
if (a == 5 ) {
print("a is five!");
} else {
print("a is not five!");
print("Bye!");
Conditional programming (if statement)
// define a custom function
function customFunction (param) {
return param * 2 ;
a = customFunction( 3 ); // call the function
Custom functions
Operator Description Example for a = 2; b = 3;
<, <= smaller than, smaller or equal to c = (a < b); // c is 1 (“true”)
, >= greater than, greater or equal to c = (a > b); // c is 0 (“false”) == equal to c = (a==b); // c is 0 (“false”) != not equal to^1 c = (a != 1 ); // c is 1 (“true”)
Conditions and logical operators
while (condition) {
// do sth at each loop iteration
// until condition is false
Iterative programming (while loop)
a b
“ AND ”: a && b
(corresp. to a*b)
“ OR ”: a || b
(~corresp. to a+b)
“ NOT ”: !a
(corresp. to 1-a)
true || true && false à 1 + 1 * 0 = 1
(true || true) && false à ( 1 + 1 ) * 0 = 0
// create arrays
v = newArray( 3 , - 4 , 0 );
// arrays can also hold strings
animals = newArray("Dog","Cat","Mouse");
// access individual array elements
v[ 0 ] = 3 ;
// NOTE: the first element has index 0!
// output arrays
Array.print(v);
// create an empty array of given size
v = newArray( 3 );
Array.print(v);
// combine arrays
mixed = Array.concat(v, animals);
// determine size of an array
numberOfElements = lengthOf(v);
Vectors / arrays
1
Iterative programming (for loop)
for (i = 0 ; i < 3 ; i++ ) {
print("i is " + i);
} start with this
before each loop: check & only continue if this is true after each loop: do this
Robert Haase (Myers lab, MPI-CBG); Benoit Lombardot, Noreen Walker and Gayathri Nadar (Scientific Computing Facility, MPI-CBG); Jens Ehrig (CMCB, TU Dresden)
Cheat sheet
ImageJ macro commands and user interfaces
Navigation in image stacks
Stack.getDimensions(width, height, channels, slices, frames); Stack.setSlice(slice); Stack.setChannel(channel); Stack.setFrame(frame); Stack.setDisplayMode("color"); Stack.setDisplayMode("composite"); Stack.setDisplayMode("grayscale");
Handle image files and folders
open(folder+imageFilename); close(); fileList = getFileList(folder); numFiles = lengthOf(fileList); for (i= 0 ;i<lengthOf(fileList);i++){ file = fileList[i]; open(file); // actual image processing... close(); }
Switch between image windows
titleOfCurrentImage = getTitle(); selectWindow(titleOfAnyImage);
Calling any ImageJ/FIJI menu
run("Enhance Contrast...", "saturated=0.3 normalize")
Best practices in developing software
Divide and rule
- Split complex issues into smaller,
accessible issues
- If a function solves several issues, split it
in separate functions.
Don’t repeat yourself (DRY)
- Don’t copy code if similar things are done
twice, because you may copy
programming errors.
- Program a loop or custom function
instead. Maintenance is easier then.
Keep it short and simple (KISS)
- develop code so that others can read,
understand and maintain it.
Variable and function names
- name functions after what they do,
(verb + object). e.g.: analyzeImage()
- name variables after what they contain,
e.g.: ("A" versus "area")
- assign parameter values at the beginning
of the script, so you do not have to search
for them once you want to change them
Result tables
run("Set Measurements...", "area mean standard min centroid"); corresp. to this: run("Analyze Particles...", "add clear display"); roiManager("Measure"); rowCount = nResults(); value = getResult("column title", rowNumber); setResult("column title", rowNumber, newValue); saveAs("Results","myResults.xls"); run("Clear results");
Ask for user action
waitForUser("headline", "prompt");
Useful links
ImageJ macro reference https://imagej.nih.gov/ij/developer/macro/macros.html https://imagej.nih.gov/ij/developer/macro/functions.html ImageJ / Fiji plugins https://imagej.net/Category:Plugins Forum http://forum.imagej.net/ Macro code auto formatter http://jsbeautifier.org/
Basic image statistics
getStatistics(area, mean, min, max, standard_deviation);
ROI manager
roiManager("add"); roiManager("split"); roiManager("delete"); roiManager("reset"); roiManager("measure"); roiManager("count"); roiManager("open", filename); roiManager("save", filename); roiManager("save selected", filename); roiManager("select", index); roiManager("select", newArray(index1, index2, ...)); roiManager("deselect"); roiManager("show all"); roiManager("show all with labels"); roiManager("show none"); roiManager("and");
Reading image calibration roiManager("combine");
getPixelSize(unit, pWidth, pHeight); getVoxelSize(vWidth, vHeight, vDepth, unit);
Generate user interfaces with #@Parameter
Syntax: #@ ()
#@ String(label="Your Text") userText #@ String(value="Some useful hints...", visibility="MESSAGE") hints #@ String(label="Analyst name", description="Your name") analystName #@ String(choices={"A", "B"}, style="radioButtonHorizontal") ROI #@ String(label="Exp. Group", choices={"Mutant", "Control"}, style="list") expGroup #@ Integer(label="Ratio 1") r #@ Integer(label="Ratio 2", value= 25 , min= 0 , max= 100 , style="slider") r #@ Double(value=0.7, min= 0 , max= 1 , label="A real number") realNumber #@ File(style="open") inputFile #@ File(style="save") outputFile #@ File(style="directory") imageFolder #@ ColorRGB(value="red") color #@ Boolean(label="Show Preview?") preview
