diff --git a/tools/jfjoch_process.cpp b/tools/jfjoch_process.cpp
index 873312a2..d15276ae 100644
--- a/tools/jfjoch_process.cpp
+++ b/tools/jfjoch_process.cpp
@@ -32,6 +32,9 @@ void print_usage(Logger &logger) {
     logger.Info("   -s<num>   Start image number (default: 0)");
     logger.Info("   -e<num>   End image number (default: all)");
     logger.Info("   -v         Verbose output");
+    logger.Info("   -R[num]   Rotation indexing (optional: min angular range deg)");
+    logger.Info("   -F         Use FFT indexing algorithm (default: Auto)");
+    logger.Info("   -x         No least-square beam center refinement");
 }
 
 int main(int argc, char **argv) {
@@ -47,7 +50,10 @@ int main(int argc, char **argv) {
     int start_image = 0;
     int end_image = -1; // -1 indicates process until end
     bool verbose = false;
-    bool rotation_index = false;
+    bool rotation_indexing = false;
+    std::optional<float> rotation_indexing_range;
+    bool use_fft = false;
+    bool refine_beam_center = true;
 
     if (argc == 1) {
         print_usage(logger);
@@ -55,7 +61,7 @@ int main(int argc, char **argv) {
     }
 
     int opt;
-    while ((opt = getopt(argc, argv, "o:N:s:e:vR")) != -1) {
+    while ((opt = getopt(argc, argv, "o:N:s:e:vR::Fx")) != -1) {
         switch (opt) {
             case 'o':
                 output_prefix = optarg;
@@ -73,7 +79,14 @@ int main(int argc, char **argv) {
                 verbose = true;
                 break;
             case 'R':
-                rotation_index = true;
+                rotation_indexing = true;
+                if (optarg) rotation_indexing_range = atof(optarg);
+                break;
+            case 'F':
+                use_fft = true;
+                break;
+            case 'x':
+                refine_beam_center = false;
                 break;
             default:
                 print_usage(logger);
@@ -117,9 +130,19 @@ int main(int argc, char **argv) {
 
     // Configure Indexing
     IndexingSettings indexing_settings;
-    indexing_settings.Algorithm(IndexingAlgorithmEnum::FFT);
-    indexing_settings.RotationIndexing(rotation_index);
-    indexing_settings.GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum::BeamCenter);
+    if (use_fft)
+        indexing_settings.Algorithm(IndexingAlgorithmEnum::FFT);
+    else
+        indexing_settings.Algorithm(IndexingAlgorithmEnum::Auto);
+
+    indexing_settings.RotationIndexing(rotation_indexing);
+    if (rotation_indexing_range.has_value())
+        indexing_settings.RotationIndexingMinAngularRange_deg(rotation_indexing_range.value());
+
+    if (refine_beam_center)
+        indexing_settings.GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum::BeamCenter);
+    else
+        indexing_settings.GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum::None);
     experiment.ImportIndexingSettings(indexing_settings);
 
     SpotFindingSettings spot_settings;