Image analysis

1) Calling ImageJ macro from the command line

/Users/administrator/Desktop/ImageJ/ImageJ64.app/Contents/MacOS/JavaApplicationStub -macro proc_Wu_1MOD.ijm /Users/administrator/Desktop/Soumya/MPI\ Work/automating_ImageJ/folders_from_a/unprocessed_TIRF_data/09_06_13_N2a_TagBFP_DA_KRC_TIRF_EGFP_D2_RacQ61L_mCherry_N1_10uM_old_ligand_10uM_competitor_10uM_Hoechst_solution_001/

where the ImageJ macro (proc_Wu_1MOD.ijm) has been placed in the macros folder for ImageJ (in this case in /Users/administrator/Desktop/ImageJ/macros).

This macro accepts an input directory as an argument.

2) Calling CellProfiler from the command line

/Applications/CellProfiler2.0.app/Contents/MacOS/CellProfiler2.0 -p /Users/administrator/Desktop/Soumya/MPI\ Work/Muthu_automation/timelapse_analysis_TRFP_control_v5_green_redobject_muthuv4.cp -i /Users/administrator/Desktop/Soumya/MPI\ Work/Muthu_automation/soumya_automationv2/ -o /Users/administrator/Desktop/Soumya/MPI\ Work/Muthu_automation/soumya_automationv2/ -r

where the name of the pipeline is timelapse_analysis_TRFP_control_v5_green_redobject_muthuv4.cp, the input directory comes after the directive -i and the output directory comes after the directive -o