diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfoHelper.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfoHelper.java
index c232e76ccc63a5cd31317a6d32878c49ccd5a202..715436e2fe85e6f934e4e1e91007ffeefd0da871 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfoHelper.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfoHelper.java
@@ -126,7 +126,7 @@ public class ScreeningContainerDatasetInfoHelper
         {
             if (updateContainer)
             {
-                dao.updateContainer(containerId, info.getContainerColumns(), info
+                dao.updateContainerEmptySpots(containerId, info.getContainerColumns(), info
                         .getContainerRows());
             }
             return new CreatedOrFetchedEntity(updateContainer == false, containerId);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingQueryDAO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingQueryDAO.java
index b2224136d0960970c97d9e94b7e30ebae325f75a..1f32a96389c23f25b88d1500f41fc037a8036d93 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingQueryDAO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingQueryDAO.java
@@ -125,8 +125,8 @@ public interface IImagingQueryDAO extends TransactionQuery
     public long addChannel(ImgChannelDTO channel);
 
     @Update("update CONTAINERS " + "set SPOTS_WIDTH = ?{2}, SPOTS_HEIGHT = ?{3} "
-            + "where ID = ?{1}")
-    public void updateContainer(long id, int columns, int rows);
+            + "where ID = ?{1} and SPOTS_WIDTH = 0 and SPOTS_HEIGHT = 0")
+    public void updateContainerEmptySpots(long id, int columns, int rows);
 
     @Select("insert into CONTAINERS (PERM_ID, SPOTS_WIDTH, SPOTS_HEIGHT, EXPE_ID) values "
             + "(?{1.permId}, ?{1.numberOfColumns}, ?{1.numberOfRows}, ?{1.experimentId}) returning ID")
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessorTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessorTest.java
index 41d7866ca741cb6c4238bc8957623b30b75df170..01517b53e7b32efd69ada696e430cac8499fd0a7 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessorTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessorTest.java
@@ -89,7 +89,7 @@ public class FeatureStorageProcessorTest extends AbstractFileSystemTestCase
                     one(dao).tryGetContainerIdPermId(CONTAINER_PERM_ID);
                     will(returnValue((long) 1));
 
-                    one(dao).updateContainer(1, 0, 0);
+                    one(dao).updateContainerEmptySpots(1, 0, 0);
                     one(dao).commit();
 
                     ImgDatasetDTO dataSetDTO = new ImgDatasetDTO(DATA_SET_PERM_ID, 3, 2, 1);