diff --git a/tools/jfjoch_process.cpp b/tools/jfjoch_process.cpp
index 21003c88..a00acd29 100644
--- a/tools/jfjoch_process.cpp
+++ b/tools/jfjoch_process.cpp
@@ -68,6 +68,7 @@ void print_usage() {
     std::cout << "   --min-partiality <num>          Minimum partiality to accept reflection (default: 0.02)" << std::endl;
     std::cout << "   --min-image-cc <num>            Per-image CC limit in percent (default: no limit)" << std::endl;
     std::cout << "   --scaling-iterations <num>      Number of scaling iterations with no reference data (default: 3)" << std::endl;
+    std::cout << "   --scaling-output <txt>              Output format for scaling results mtz|cif|txt (default: mtz)" << std::endl;
     std::cout << "   -z, --reference-mtz <file>      Reference MTZ file" << std::endl;
     }
 
@@ -80,7 +81,8 @@ enum {
     OPT_MIN_PARTIALITY,
     OPT_MIN_IMAGE_CC,
     OPT_SCALING_ITERATIONS,
-    OPT_SCALING_HIGH_RESOLUTION
+    OPT_SCALING_HIGH_RESOLUTION,
+    OPT_SCALING_OUTPUT
 };
 
 static option long_options[] = {
@@ -110,7 +112,7 @@ static option long_options[] = {
     {"min-image-cc", required_argument, nullptr, OPT_MIN_IMAGE_CC},
     {"scaling-iterations", required_argument, nullptr, OPT_SCALING_ITERATIONS},
     {"scaling-high-resolution", required_argument, nullptr, OPT_SCALING_HIGH_RESOLUTION},
-
+    {"scaling-output", required_argument, nullptr, OPT_SCALING_OUTPUT},
     {nullptr, 0, nullptr, 0}
 };
 
@@ -215,6 +217,7 @@ int main(int argc, char **argv) {
 
     IndexingAlgorithmEnum indexing_algorithm = IndexingAlgorithmEnum::Auto;
 
+    IntensityFormat intensity_format = IntensityFormat::MTZ;
     PartialityModel partiality_model = PartialityModel::Fixed;
 
     float d_min_spot_finding = 1.5;
@@ -355,6 +358,18 @@ int main(int argc, char **argv) {
         case OPT_SCALING_HIGH_RESOLUTION:
             d_min_scale_merge = atof(optarg);
             break;
+        case OPT_SCALING_OUTPUT:
+            if (strcmp(optarg, "mtz") == 0) {
+                intensity_format = IntensityFormat::MTZ;
+            } else if (strcmp(optarg, "cif") == 0) {
+                intensity_format = IntensityFormat::mmCIF;
+            } else if (strcmp(optarg, "txt") == 0) {
+                intensity_format = IntensityFormat::Text;
+            } else {
+                logger.Error("Invalid intensity format: {}", optarg);
+                exit(EXIT_FAILURE);
+            }
+            break;
         case OPT_SCALING_ITERATIONS:
             scaling_iter = atoi(optarg);
             if (scaling_iter <= 0) {
@@ -477,6 +492,7 @@ int main(int argc, char **argv) {
         scaling_settings.RotationWedgeForScaling(wedge_for_scaling);
     scaling_settings.MinPartiality(min_partiality);
     scaling_settings.MinCCForImage(min_image_cc);
+    scaling_settings.FileFormat(intensity_format);
 
     experiment.ImportScalingSettings(scaling_settings);
 
diff --git a/tools/jfjoch_scale.cpp b/tools/jfjoch_scale.cpp
index e9807260..61052990 100644
--- a/tools/jfjoch_scale.cpp
+++ b/tools/jfjoch_scale.cpp
@@ -3,25 +3,18 @@
 
 #include <iostream>
 #include <vector>
-#include <string>
-#include <unistd.h>
+#include <string>[]
 #include <future>
-#include <mutex>
-#include <atomic>
 #include <chrono>
 #include <fstream>
-#include <sstream>
 #include <getopt.h>
 
 #include "../reader/JFJochHDF5Reader.h"
 #include "../common/Logger.h"
 #include "../common/DiffractionExperiment.h"
-#include "../common/PixelMask.h"
-#include "../common/AzimuthalIntegrationMapping.h"
 #include "../common/time_utc.h"
 #include "../common/print_license.h"
 #include "../image_analysis/MXAnalysisWithoutFPGA.h"
-#include "../image_analysis/indexing/IndexerFactory.h"
 #include "../writer/FileWriter.h"
 #include "../image_analysis/IndexAndRefine.h"
 #include "../receiver/JFJochReceiverPlots.h"
@@ -57,13 +50,15 @@ void print_usage() {
     std::cout << "   --min-image-cc <num>              Per-image CC limit in percent (default: no limit)" << std::endl;
     std::cout << "   --scaling-iterations <num>        Number of scaling iterations with no reference data (default: 3)"
             << std::endl;
+    std::cout << "   --scaling-output <txt>              Output format for scaling results mtz|cif|txt (default: mtz)" << std::endl;
     std::cout << "   -z, --reference-mtz <file>            Reference MTZ file" << std::endl;
 }
 
 enum {
     OPT_MIN_PARTIALITY = 1000,
     OPT_MIN_IMAGE_CC,
-    OPT_SCALING_ITERATIONS
+    OPT_SCALING_ITERATIONS,
+    OPT_SCALING_OUTPUT
 };
 
 
@@ -83,6 +78,7 @@ static option long_options[] = {
     {"min-partiality", required_argument, nullptr, OPT_MIN_PARTIALITY},
     {"min-image-cc", required_argument, nullptr, OPT_MIN_IMAGE_CC},
     {"scaling-iterations", required_argument, nullptr, OPT_SCALING_ITERATIONS},
+    {"scaling-output", required_argument, nullptr, OPT_SCALING_OUTPUT},
     {nullptr, 0, nullptr, 0}
 };
 
@@ -109,6 +105,7 @@ int main(int argc, char **argv) {
     double min_image_cc = 0.0;
     int64_t scaling_iter = 3;
 
+    IntensityFormat intensity_format = IntensityFormat::MTZ;
     PartialityModel partiality_model = PartialityModel::Fixed;
 
     std::optional<float> d_min_scale_merge;
@@ -179,6 +176,18 @@ int main(int argc, char **argv) {
             case OPT_MIN_IMAGE_CC:
                 min_image_cc = std::stod(optarg);
                 break;
+            case OPT_SCALING_OUTPUT:
+                if (strcmp(optarg, "mtz") == 0) {
+                    intensity_format = IntensityFormat::MTZ;
+                } else if (strcmp(optarg, "cif") == 0) {
+                    intensity_format = IntensityFormat::mmCIF;
+                } else if (strcmp(optarg, "txt") == 0) {
+                    intensity_format = IntensityFormat::Text;
+                } else {
+                    logger.Error("Invalid intensity format: {}", optarg);
+                    exit(EXIT_FAILURE);
+                }
+                break;
             case OPT_SCALING_ITERATIONS:
                 scaling_iter = atoi(optarg);
                 if (scaling_iter <= 0) {
@@ -274,6 +283,7 @@ int main(int argc, char **argv) {
         scaling_settings.RotationWedgeForScaling(wedge_for_scaling);
     scaling_settings.MinPartiality(min_partiality);
     scaling_settings.MinCCForImage(min_image_cc);
+    scaling_settings.FileFormat(intensity_format);
 
     experiment.ImportScalingSettings(scaling_settings);