diff --git a/fishbook/backend/database.py b/fishbook/backend/database.py
index 592caca..f642af9 100644
--- a/fishbook/backend/database.py
+++ b/fishbook/backend/database.py
@@ -453,7 +453,9 @@ def scan_nix_file_for_repros(dataset):
 def scan_folder_for_repros(dataset):
     print("\t\tNo nix-file, scanning directory!")
     repro_settings, stim_indices = read_stimuli_file(dataset["data_source"])
-    repro_counts = {}
+    repro_counts = {}  # internal counter for repro runs, for cases in which the repro does not have a run counter
+    repros_skipped = {}  # internal counter to correct the run counter for repro runs in which no stimulus was put out, needed to align e.g. with stimspikes file
+    repros_without_stims = ["baselineactivity"]
     cell_id = (Cells * CellDatasetMap * (Datasets & "dataset_id = '%s'" % dataset["dataset_id"])).fetch("cell_id", limit=1)[0]
     for rs, si in zip(repro_settings, stim_indices):
         rp = Repros.get_template_tuple()
@@ -463,20 +465,26 @@ def scan_folder_for_repros(dataset):
             find_key_recursive(rs, "RePro", path)
         rp["repro_name"] = deep_get(rs, path, "None")
         
+        if rp["repro_name"] not in repros_skipped.keys():
+            repros_skipped[rp["repro_name"]] = 0
+
+        if rp["repro_name"].lower() not in repros_without_stims and len(si) == 0:
+            repros_skipped[rp["repro_name"]] += 1        
+            continue
+    
         path = []
         if rp["repro_name"] in repro_counts.keys():
             repro_counts[rp["repro_name"]] += 1
         else:
             repro_counts[rp["repro_name"]] = 0
-        
         path = []      
         if not find_key_recursive(rs, "run", path):
             find_key_recursive(rs, "Run", path)
         if len(path) > 0:
-            rp["run"] = deep_get(rs, path, 0)
+            rp["run"] = int(deep_get(rs, path, 0)) - repros_skipped[rp["repro_name"]]
         else: # the run information is not there and needs to be fixed!
-            rp["run"] = repro_counts[rp["repro_name"]]    
-        
+            rp["run"] = repro_counts[rp["repro_name"]] - repros_skipped[rp["repro_name"]]
+
         rp["cell_id"] = cell_id
         rp["repro_id"] = rp["repro_name"] + str(repro_counts[rp["repro_name"]])
         rp["start"] = 0.
@@ -501,8 +509,10 @@ def scan_folder_for_repros(dataset):
                 find_key_recursive(rs, "Duration", path)
             if len(path) > 0 :
                 stim_duration = deep_get(rs, path, None)
-                if "ms" in stim_duration:
-                    stim_duration = float(stim_duration[:stim_duration.index("ms")])
+                if "sec" in stim_duration:
+                    stim_duration = float(stim_duration[:stim_duration.index("sec")])
+                elif "ms" in stim_duration:
+                    stim_duration = float(stim_duration[:stim_duration.index("ms")]) / 1000
                 else:
                     stim_duration = float(stim_duration[:stim_duration.index("s")])
             else:
diff --git a/fishbook/frontend/util.py b/fishbook/frontend/util.py
index b8e2665..234dee0 100644
--- a/fishbook/frontend/util.py
+++ b/fishbook/frontend/util.py
@@ -207,7 +207,16 @@ class StimSpikesFile:
         for l in lines:
             l = l.strip()
             if "duration:" in l:
-                trial_duration = float(l[1:].strip().split(":")[-1][:-3])
+                trial_duration = l[1:].strip().split(":")[-1].strip()
+                if "sec" in trial_duration:
+                    trial_duration = float(trial_duration[:-3])
+                elif "ms" in trial_duration:
+                    trial_duration = float(trial_duration[:-2]) / 1000
+                elif trial_duration[-1] == 's':
+                    trial_duration = float(trial_duration[:1])
+                else:
+                    trial_duration = 0.0
+                print(l, trial_duration)
             if "index:" in l:
                 if len(trial_data) > 0:
                     index_map[(index, trial)] = (trial_duration, trial_data)