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Fiji examples

MontageFlyBrain

Find a few examples to get productive using Fiji and your images:

1) Open one image:

inputdir = "/global/scratch2/sd/youname/";
open(inputdir + "myExperiment001.tif");

2) Reading a collection of 2D images:

numberfiles=38;
filename = "myExperiment";
startfile=1;
run("Image Sequence...", "open=["+inputdir+"] number="+numberfiles+" starting="+startfile+" increment=1 scale=100 file="+filename+" or=[] convert sort");

3) Visualizing/snapshotting content:

run("Make Montage...", "columns=9 rows=7 scale=0.25 first=1 last=57 increment=1 border=0 font=12 label use");
saveAs("PNG", "/global/scratch2/sd/ushizima/MontageFlyBrain.png"); 

4) Making a movie out of your 3D dataset: if your input image presents enough contrast, e.g. segmented objects, you can view the outer shell through projections of the object from several different angles.

run("Bat Cochlea Volume (19K)");
run("3D Project...", "projection=[Brightest Point]
axis=Y-Axis slice=1 initial=0 total=360 rotation=10 lower=1 upper=255 opacity=10 surface=100 interior=50 interpolate");
doCommand("Start Animation [\\]");
saveAs("Gif", ""/global/scratch2/sd/ushizima/Projections of bat-cochlea-volume.gif");

5) ImageJ 3D Viewer - OpenGL-solution for Fiji

run("T1 Head (2.4M, 16-bits)");
run("3D Viewer");
call("ij3d.ImageJ3DViewer.setTransparency", "0.86");

6) Checking image attributes, metadata, pixel depth, and other valuable parameters

run("HeLa Cells (1.3M, 48-bit RGB)");
run("Show Info...");

7) Image filtering using non-linear filters

run("Cell Colony (31K)");
run("Anisotropic Diffusion 2D", "number=20 smoothings=1 keep=20 a1=0.50 a2=0.90 dt=20 edge=5");

 8) Segmenting, counting, measuring image from wells of a glass micromodel and labeling of detected wells

run("Split Channels");
selectWindow("micromodel.png (green)");
run("Analyze Particles...", "size=100-Infinity circularity=0.85-1.00 show=Outlines display in_situ");
setAutoThreshold("MaxEntropy dark");
run("Threshold...");
run("Analyze Particles...", "size=100-Infinity circularity=0.85-1.00 show=Outlines display in_situ");
saveAs("Results",inputdir+”Results.xls");

9) Calling macros at the command line

 

<fiji-bin-path> --headless -macro "macroName.ijm" inputData.jpg -batch

 

 

Other resources:  How_to_apply_a_common_operation_to_a_complete_directory