Update docs

examples/import.ijm

@@ -1,7 +1,17 @@
-#@ File (label = "Input file", style = "file") input
-// input = "/absolute/path/to/some/directory/src/test/resources/2d_cells_apoptotic_1channel.h5";
+// Lines that start with "//" are comments.
+
+// Lines that start with "#@" declare input parameters that interactively ask the user for values.
+// You can remove those lines and set input parameters explicitly in order to run the macro without further user interaction.
+
+#@ File (label = "Input file", style = "directory") dataDir
+// dataDir = "/absolute/path/to/some/directory/with/h5-files/";
 
 datasetname = "/data";
 axisorder = "tzyxc";
 
-run("Import HDF5", "select=[" + input + "] datasetname=[" + datasetname + "] axisorder=[" + axisorder + "]");
+fileList = getFileList(dataDir);
+for (i = 0; i < fileList.length; i++) {
+  // import image from the H5
+  fileName = dataDir + fileList[i];
+  run("Import HDF5", "select=[" + fileName + "] datasetname=[" + datasetname + "] axisorder=[" + axisorder + "]");
+}

examples/multicut.ijm

@@ -0,0 +1,19 @@
+// Lines that start with "//" are comments.
+
+// Lines that start with "#@" declare input parameters that interactively ask the user for values.
+// You can remove those lines and set input parameters explicitly in order to run the macro without further user interaction.
+
+#@ File (label = "Project file", style = "file") project
+// project = "/absolute/path/to/some/directory/multicut.ilp";
+
+#@ File (label = "Input file", style = "file") input
+// input = "/absolute/path/to/some/directory/raw_data.tif";
+
+#@ File (label = "Second input file", style = "file") secondInput
+// secondInput = "/absolute/path/to/some/directory/boundary_Probabilities.tif";
+
+type = "Probabilities";
+
+open(input);
+open(secondInput);
+run("Run Multicut", "projectfilename=[" + input + "] boundarypredictionimage=[" + secondInput +"]");

examples/object_classification.ijm

@@ -1,3 +1,8 @@
+// Lines that start with "//" are comments.
+
+// Lines that start with "#@" declare input parameters that interactively ask the user for values.
+// You can remove those lines and set input parameters explicitly in order to run the macro without further user interaction.
+
 #@ File (label = "Project file", style = "file") project
 // project = "/absolute/path/to/some/directory/obj_class_2d_cells_apoptotic.ilp";
 
@@ -10,4 +15,6 @@
 type = "Probabilities";
 
 open(input);
+open(secondInput);
+
 run("Run Object Classification Prediction", "projectfilename=[" + project + "] input=[" + input + "] inputproborsegimage=[" + secondInput + "] secondinputtype=[" + type + "]");

examples/pixel_classification.ijm

@@ -1,10 +1,36 @@
-#@ File (label = "Project file", style = "file") project
+// Lines that start with "//" are comments.
+
+// Lines that start with "#@" declare input parameters that interactively ask the user for values.
+// You can remove those lines and set input parameters explicitly in order to run the macro without further user interaction.
+
+#@ File (label = "Project file", style = "file") pixelClassificationProject
 // project = "/absolute/path/to/some/directory/pixel_class_2d_cells_apoptotic.ilp";
 
-#@ File (label = "Input file", style = "file") input
-// input = "/absolute/path/to/some/directory/2d_cells_apoptotic.tif";
+#@ File (label = "Input file", style = "directory") dataDir
+// dataDir = "/absolute/path/to/some/directory/";
+
+// set global variables
+outputType = "Probabilities"; //  or "Segmentation"
+inputDataset = "data";
+outputDataset = "exported_data";
+axisOrder = "tzyxc";
+compressionLevel = 0;
+
+// process all H5 files in a given directory
+fileList = getFileList(dataDir);
+for (i = 0; i < fileList.length; i++) {
+    // import image from the H5
+    fileName = dataDir + fileList[i];   
+    importArgs = "select=" + fileName + " datasetname=" + inputDataset + " axisorder=" + axisOrder;             
+    run("Import HDF5", importArgs);
 
-type = "Probabilities";
+    // run pixel classification
+    inputImage = fileName + "/" + inputDataset;
+    pixelClassificationArgs = "projectfilename=" + pixelClassificationProject + " saveonly=false inputimage=" + inputImage + " pixelclassificationtype=" + outputType;
+    run("Run Pixel Classification Prediction", pixelClassificationArgs);
 
-open(input);
-run("Run Pixel Classification Prediction", "projectfilename=[" + project + "] input=[" + input + "] pixelclassificationtype=[" + type + "]");
+    // export probability maps to H5
+    outputFile = dataDir + "output" + i + ".h5";
+    exportArgs = "select=" + outputFile + " datasetname=" + outputDataset + " compressionlevel=" + compressionLevel;
+    run("Export HDF5", exportArgs);
+}

examples/tracking.ijm

@@ -0,0 +1,20 @@
+// Lines that start with "//" are comments.
+
+// Lines that start with "#@" declare input parameters that interactively ask the user for values.
+// You can remove those lines and set input parameters explicitly in order to run the macro without further user interaction.
+
+#@ File (label = "Project file", style = "file") project
+// project = "/absolute/path/to/some/directory/tracking.ilp";
+
+#@ File (label = "Input file", style = "file") input
+// input = "/absolute/path/to/some/directory/raw_data.tif";
+
+#@ File (label = "Second input file", style = "file") secondInput
+// secondInput = "/absolute/path/to/some/directory/probabilities.tif";
+
+type = "Probabilities";
+
+open(input);
+open(secondInput);
+
+run("Run Tracking", "projectfilename=[" + project + "] input=[" + input + "] inputproborsegimage=[" + secondInput + "] secondinputtype=[" + type + "]");