diff --git a/spim_registration/timelapse/cluster.json b/spim_registration/timelapse/cluster.json index ab4d912db15f4f01a47972356c2ecff5629b46d6..00b1765aec32bb087004aecfff9f3281ee576c20 100755 --- a/spim_registration/timelapse/cluster.json +++ b/spim_registration/timelapse/cluster.json @@ -27,7 +27,7 @@ "fusion" : { - "lsf_extra" : "-n 6 -R \"span[hosts=1] rusage[mem=100000]\"" + "lsf_extra" : "-n 7 -R \"span[hosts=1] rusage[mem=100000]\"" }, "deconvolution" : diff --git a/spim_registration/timelapse/fusion.bsh b/spim_registration/timelapse/fusion.bsh index 945556cf0c05b6e5cec8419eb89815cc3b504338..e6050025af0a6dff457f6b50afdf1f14b2cad9d5 100755 --- a/spim_registration/timelapse/fusion.bsh +++ b/spim_registration/timelapse/fusion.bsh @@ -98,7 +98,7 @@ IJ.run("Fuse/Deconvolve Dataset", "imglib2_container=" + imglib2_container_fusion + " " + "process_views_in_paralell=All " + "interpolation=[" + interpolation + "] " + - "blend " + + //"blend " + "content-based " + "output_file_directory=" + image_file_directory + " " + "lossless " + diff --git a/spim_registration/timelapse/single_test.yaml b/spim_registration/timelapse/single_test.yaml index 9171d0c8a9537778c6c99f453f9dc12933933e86..5cf7c442522c9af81fed403730c5fb71b59a5d32 100755 --- a/spim_registration/timelapse/single_test.yaml +++ b/spim_registration/timelapse/single_test.yaml @@ -7,9 +7,9 @@ common: { fiji-app: "/sw/users/schmied/packages/2015-06-30_Fiji.app.cuda/ImageJ-linux64", fiji-prefix: "/sw/users/schmied/packages/xvfb-run -a", # calls xvfb for Fiji headless mode # xml file names without .xml suffix - first_xml_filename: '"single"', # Name of the xml file for the .czi or .tif files + first_xml_filename: 'single', # Name of the xml file for the .czi or .tif files hdf5_xml_filename: '"hdf5_single"', # Name of .xml file for the hdf5 data after resave_hdf5 - merged_xml: '"hdf5_single_merge"', # Name of .xml file after merge + merged_xml: 'hdf5_single_merge', # Name of .xml file after merge # Describe the dataset ntimepoints: 2, # number of timepoints of dataset angles: "0,72,144,216,288", # angles