Complete example for FMI dataset, with illumination correction and new channel scheme (ref #61 #62)

Author: tcompa

examples/example_fmi_2_well_4x5_sites.sh

@@ -40,6 +40,16 @@ $CMD task add yokogawa_to_zarr zarr zarr well
 $CMD task list
 echo
 
+echo 'Add replicate_zarr_structure'
+$CMD task add replicate_zarr_structure zarr zarr plate
+$CMD task list
+echo
+
+echo 'Add illumination_correction'
+$CMD task add illumination_correction zarr zarr well
+$CMD task list
+echo
+
 echo 'Add replicate_zarr_structure_mip'
 $CMD task add replicate_zarr_structure_mip zarr zarr plate
 $CMD task list
@@ -50,6 +60,8 @@ $CMD task add maximum_intensity_projection zarr zarr well
 $CMD task list
 echo
 
+#############################################
+
 echo 'Create workflow'
 $CMD workflow new mwe-test wftest create_zarr_structure
 $CMD workflow list mwe-test
@@ -60,6 +72,16 @@ $CMD workflow add-task mwe-test wftest yokogawa_to_zarr
 $CMD workflow list mwe-test
 echo
 
+#echo 'Add replicate_zarr_structure'
+#$CMD workflow add-task mwe-test wftest replicate_zarr_structure
+#$CMD workflow list mwe-test
+#echo
+
+echo 'Add illumination_correction'
+$CMD workflow add-task mwe-test wftest illumination_correction
+$CMD workflow list mwe-test
+echo
+
 echo 'Add replicate_zarr_structure_mip'
 $CMD workflow add-task mwe-test wftest replicate_zarr_structure_mip
 $CMD workflow list mwe-test

examples/wf_params_fmi_2_well_4x5_sites.json

@@ -1,8 +1,9 @@
 {
 "workflow_name": "fmi_2_well_4x5_sites",
 "dims": [4, 5],
-"coarsening_xy": 2,
+"coarsening_xy": 3,
 "coarsening_z": 1,
 "num_levels": 5,
-"channel_file": "wf_params_fmi_2_well_4x5_sites_channels.json"
+"channel_file": "wf_params_fmi_2_well_4x5_sites_channels.json",
+"path_dict_corr": "wf_params_fmi_2_well_4x5_sites_illumination.json"
 }

examples/wf_params_fmi_2_well_4x5_sites_illumination.json

@@ -0,0 +1,7 @@
+{
+    "root_path_corr": "/data/active/fractal/Liberali/FractalTesting20220124/IlluminationCorrectionMatrices-Yokogawa/",
+    "A04_C01": "220120_60xW_BP445_CH01.tif",
+    "A03_C02": "220120_60xW_BP525_CH02.tif",
+    "A02_C03": "220120_60xW_BP600_CH03.tif",
+    "A01_C04": "220120_60xW_BP600_CH03.tif"
+}