diff --git a/Detectors/ITSMFT/ITS/workflow/include/ITSWorkflow/ThresholdCalibratorSpec.h b/Detectors/ITSMFT/ITS/workflow/include/ITSWorkflow/ThresholdCalibratorSpec.h
index a5064db424e5e..6bbf6a910c1f4 100644
--- a/Detectors/ITSMFT/ITS/workflow/include/ITSWorkflow/ThresholdCalibratorSpec.h
+++ b/Detectors/ITSMFT/ITS/workflow/include/ITSWorkflow/ThresholdCalibratorSpec.h
@@ -131,7 +131,8 @@ class ITSThresholdCalibrator : public Task
  private:
   void updateTimeDependentParams(ProcessingContext& pc);
   // detector information
-  static constexpr short int N_COL = 1024; // column number in Alpide chip
+  static constexpr short int N_COL = 1024; // number of columns in Alpide chip
+  static constexpr short int N_ROW = 512;  // number of rows in Alpide chip
 
   static const short int N_RU = o2::itsmft::ChipMappingITS::getNRUs();
 
@@ -231,7 +232,8 @@ class ITSThresholdCalibrator : public Task
   short int mRunType = -1;
   short int mRunTypeUp = -1;
   short int mRunTypeRU[N_RU] = {0};
-  short int mCdwCntRU[N_RU] = {0};
+  short int mRunTypeRUCopy[N_RU] = {0};
+  short int mCdwCntRU[N_RU][N_ROW] = {{0}};
   short int mRowRU[N_RU] = {0};
   bool mActiveLinks[N_RU][3] = {{false}};
   std::set<short int> mRuSet;
diff --git a/Detectors/ITSMFT/ITS/workflow/src/ThresholdCalibratorSpec.cxx b/Detectors/ITSMFT/ITS/workflow/src/ThresholdCalibratorSpec.cxx
index 0b3d67e515360..64fa4247d8aad 100644
--- a/Detectors/ITSMFT/ITS/workflow/src/ThresholdCalibratorSpec.cxx
+++ b/Detectors/ITSMFT/ITS/workflow/src/ThresholdCalibratorSpec.cxx
@@ -1338,6 +1338,7 @@ void ITSThresholdCalibrator::run(ProcessingContext& pc)
         // count the zeros
         if (!mRunTypeUp) {
           mRunTypeRU[iRU]++;
+          mRunTypeRUCopy[iRU]++;
         }
         // Divide calibration word (24-bit) by 2^16 to get the first 8 bits
         if (this->mScanType == 'T') {
@@ -1361,7 +1362,7 @@ void ITSThresholdCalibrator::run(ProcessingContext& pc)
         // count the last N injections
         short int checkVal = (mScanType == 'I') ? mMin : mMax;
         if (loopval == checkVal && realcharge == mMin2) { // the second condition is relevant only for mScanType=p
-          mCdwCntRU[iRU]++;
+          mCdwCntRU[iRU][row]++;
           mRowRU[iRU] = row; // keep the row
         }
         if (this->mVerboseOutput) {
@@ -1476,16 +1477,17 @@ void ITSThresholdCalibrator::run(ProcessingContext& pc)
     }
     std::vector<short int> chipEnabled = getChipListFromRu(iRU, mActiveLinks[iRU]); // chip boundaries
     // Fill the chipDone info string
-    if (mRunTypeRU[iRU] == nInjScaled * nL) {
+    if (mRunTypeRUCopy[iRU] == nInjScaled * nL) {
       for (short int iChip = 0; iChip < chipEnabled.size(); iChip++) {
         if ((chipEnabled[iChip] % mChipModBase) != mChipModSel) {
           continue;
         }
         addDatabaseEntry(chipEnabled[iChip], "", std::vector<float>(), true);
       }
+      mRunTypeRUCopy[iRU] = 0; // reset here is safer (the other counter is reset in finalize)
     }
     // Check if scan of a row is finished: only for specific scans!
-    bool passCondition = (mCdwCntRU[iRU] == nInjScaled * nL);
+    bool passCondition = (mCdwCntRU[iRU][mRowRU[iRU]] >= nInjScaled * nL);
     if (mScanType != 'D' && mScanType != 'A' && mScanType != 'P' && mScanType != 'p' && mScanType != 'R' && mScanType != 'r' && passCondition) {
       // extract data from the row
       for (short int iChip = 0; iChip < chipEnabled.size(); iChip++) {
@@ -1503,7 +1505,7 @@ void ITSThresholdCalibrator::run(ProcessingContext& pc)
           }
         }
       }
-      mCdwCntRU[iRU] = 0; // reset
+      mCdwCntRU[iRU][mRowRU[iRU]] = 0; // reset
     }
   } // end loop on RuSet