diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt
index f43016e3..d317c914 100644
--- a/tools/CMakeLists.txt
+++ b/tools/CMakeLists.txt
@@ -35,10 +35,6 @@ ADD_EXECUTABLE(jfjoch_lite_perf_test jfjoch_lite_perf_test.cpp)
 TARGET_LINK_LIBRARIES(jfjoch_lite_perf_test JFJochReceiver JFJochWriter)
 INSTALL(TARGETS jfjoch_lite_perf_test RUNTIME COMPONENT jfjoch)
 
-ADD_EXECUTABLE(jfjoch_indexing_test jfjoch_indexing_test.cpp)
-TARGET_LINK_LIBRARIES(jfjoch_indexing_test JFJochReader JFJochImageAnalysis JFJochWriter)
-INSTALL(TARGETS jfjoch_indexing_test RUNTIME COMPONENT jfjoch)
-
 ADD_EXECUTABLE(jfjoch_extract_hkl jfjoch_extract_hkl.cpp
         XdsIntegrateParser.cpp
         XdsIntegrateParser.h)
diff --git a/tools/jfjoch_indexing_test.cpp b/tools/jfjoch_indexing_test.cpp
deleted file mode 100644
index 01740474..00000000
--- a/tools/jfjoch_indexing_test.cpp
+++ /dev/null
@@ -1,73 +0,0 @@
-// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
-// SPDX-License-Identifier: GPL-3.0-only
-
-#include "../reader/JFJochHDF5Reader.h"
-#include "../image_analysis/indexing/IndexerFactory.h"
-#include "../common/Logger.h"
-#include "../image_analysis/IndexAndRefine.h"
-#include "../image_analysis/bragg_prediction/BraggPredictionFactory.h"
-#include "../writer/FileWriter.h"
-#include "../image_analysis/indexing/AnalyzeIndexing.h"
-
-int main(int argc, char** argv) {
-    Logger logger("jfjoch_indexing_test");
-
-    if (argc != 2) {
-        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Usage: ./jfjoch_indexing_test <file>");
-    }
-
-    JFJochHDF5Reader reader;
-    reader.ReadFile(argv[1]);
-    if (!reader.GetDataset())
-        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Error opening file");
-
-    IndexingSettings indexing_settings;
-    indexing_settings.Algorithm(IndexingAlgorithmEnum::FFT);
-    indexing_settings.RotationIndexing(true);
-    indexing_settings.GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum::BeamCenter);
-    DiffractionExperiment experiment(reader.GetDataset()->experiment);
-    experiment.ImportIndexingSettings(indexing_settings);
-    experiment.SetUnitCell({});
-    experiment.FilePrefix("output");
-
-    StartMessage msg;
-    experiment.FillMessage(msg);
-    // FileWriter fw(msg);
-
-    IndexerThreadPool indexer(experiment.GetIndexingSettings());
-    SpotFindingSettings settings{};
-    settings.quick_integration = false;
-    settings.indexing = true;
-
-    auto geom = experiment.GetDiffractionGeometry();
-    IndexAndRefine rot_index(experiment, &indexer);
-
-    auto prediction = CreateBraggPrediction();
-
-    int cnt = 0;
-    for (int i = 0; i < reader.GetNumberOfImages(); i++) {
-        auto img = reader.LoadImage(i);
-
-        if (!img)
-            continue;
-
-        DataMessage msg = img->ImageData();
-
-        rot_index.ProcessImage(msg, settings, msg.image, *prediction);
-
-        if (msg.indexing_result && msg.indexing_result.value())
-            cnt++;
-
-        if (i % 200 == 0)
-            logger.Info("Image {} {}", i, cnt);
-
-    }
-    auto latt_1 = rot_index.Finalize();
-    if (latt_1) {
-        auto uc = latt_1->lattice.GetUnitCell();
-        logger.Info("Unit cell {} {} {} {} {} {}", uc.a, uc.b, uc.c, uc.alpha, uc.beta, uc.gamma);
-        logger.Info("Latt1 {} {} {}", latt_1->lattice.Vec0().x, latt_1->lattice.Vec0().y, latt_1->lattice.Vec0().z);
-        logger.Info("Latt1 {} {} {}", latt_1->lattice.Vec1().x, latt_1->lattice.Vec1().y, latt_1->lattice.Vec1().z);
-        logger.Info("Latt1 {} {} {}", latt_1->lattice.Vec2().x, latt_1->lattice.Vec2().y, latt_1->lattice.Vec2().z);
-    }
-}
\ No newline at end of file