pconesa / bunwarpj_code

This ImageJ/Fiji plugin performs 2D image registration based on elastic deformations represented by B-splines. The invertibility of the deformations is enforced through a consistency restriction.

bUnwarpJ_code

This ImageJ/Fiji plugin performs 2D image registration based on elastic deformations represented by B-splines. The invertibility of the deformations is enforced through a consistency restriction.

Running ImageJ/Fiji with Multiple parameters

• Command on Linux: ./ImageJ-linux64 --ij2 --headless --run "hello.py" "name1='Mr',name2='Mrs Kraken'"

Running bUnwarpJ_code in headless mode through Linux Terminal

/path/to/ImageJ-linux64 --ij2 --headless --run "/path/to/groovyscript/bUnwarpJ_Ana.groovy" "inputFile='/path/to/inputFiles/image',beadsFile='/path/to/beadsFile/beadsImage',outputDir='/path/to/outputFolder/results',fixedCh=0,headless=true"

Running bUnwarpJ_code in headless mode (my parameters) through Linux Terminal

/home/anaacayuela/Desktop/fiji-linux64/Fiji.app/ImageJ-linux64 --ij2 --headless --run "/home/anaacayuela/Ana_pruebas_imageJ/bUnwarpJ/groovy/src/main/bUnwarpJ_Ana.groovy" "inputFile='/home/anaacayuela/Ana_pruebas_imageJ/bUnwarpJ/paper/set_2/images/Sylvia Gutierrez-Erlandsson - Hoechst 1x_34ºC.lif',beadsFile='/home/anaacayuela/Ana_pruebas_imageJ/bUnwarpJ/paper/set_2/ref_beads/Sylvia Gutierrez-Erlandsson - Beads ref.lif',outputDir='/home/anaacayuela/Ana_pruebas_imageJ/bUnwarpJ/paper/set_2/results',fixedCh=0,headless=true"

Optionally Avanced Parameters for elastic registration can be set as arguments:

• #@Integer(label="Registration Mode", value=1) mode
• #@Integer(label="Image Subsample Factor", value=0) img_subsamp_fact
• #@Integer(label="Initial Deformation", value=0) min_scale_deformation
• #@Integer(label="Final Deformation", value=2) max_scale_deformation
• #@Double(label="Divergence Weight", value=0.0) divWeight
• #@Double(label="Curl Weight", value=0.0) curlWeight
• #@Double(label="Landmark Weight", value=0.0) landmarkWeight
• #@Double(label="Image Weight", value=1.0) imageWeight
• #@Double(label="Consistency Weight", value=10.0) consistencyWeight
• #@Double(label="Stop Threshold", value=0.01) stopThreshold