From 92ceb73db10914102a996b536d45b3239f558c90 Mon Sep 17 00:00:00 2001
From: beccawhitaker <beccamwhitaker@gmail.com>
Date: Fri, 27 Feb 2026 10:59:10 -0500
Subject: [PATCH 1/2] Update batchDetectSpikes.m

allow negative absolute thresholds to be read as a string (hyphen to underscore)
---
 Functions/WATERS-master/batchDetectSpikes.m | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/Functions/WATERS-master/batchDetectSpikes.m b/Functions/WATERS-master/batchDetectSpikes.m
index 5d645ed..6d27452 100644
--- a/Functions/WATERS-master/batchDetectSpikes.m
+++ b/Functions/WATERS-master/batchDetectSpikes.m
@@ -282,6 +282,9 @@ function batchDetectSpikes(dataPath, savePath, option, files, Params, MEANAPapp)
                     wname = char(wnameList{wname});
                     valid_wname = strrep(wname, '.', 'p');
                     actual_wname = strrep(wname, 'p', '.');
+                    if contains(wname, '-')
+                        valid_wname = strrep(wname, '-', '_');
+                    end
                     
                     spikeWaves = [];
                     spikeFrames = [];

From b510469b3e968fe208aa83b78fbfcfae5130a055 Mon Sep 17 00:00:00 2001
From: beccawhitaker <beccamwhitaker@gmail.com>
Date: Fri, 27 Feb 2026 11:03:45 -0500
Subject: [PATCH 2/2] Update detectSpikesCWT.m

absthr edits
---
 Functions/WATERS-master/detectSpikesCWT.m | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/Functions/WATERS-master/detectSpikesCWT.m b/Functions/WATERS-master/detectSpikesCWT.m
index 5d357f7..be6b08d 100644
--- a/Functions/WATERS-master/detectSpikesCWT.m
+++ b/Functions/WATERS-master/detectSpikesCWT.m
@@ -157,11 +157,18 @@
 
 elseif startsWith(wname, 'absthr')
     absThreshold = strrep(wname, 'p', '.');
-    absThreshold = strrep(absThreshold, 'thr', '');
-    absThreshold = str2num(absThreshold);
+    absThreshold = strrep(absThreshold, 'absthr', '');
+    absThreshold = str2double(absThreshold);
     [spikeTrain, ~, ~] = detectSpikesThreshold(trace, 0, refPeriod, fs, 0, absThreshold, threshold_calculation_window);
     spikeTimes = find(spikeTrain == 1);
     threshold = absThreshold;
+
+     % Align spikes by negative peak & remove artifacts by amplitude
+    [spikeTimes, spikeWaveforms] = alignPeaks(spikeTimes, trace, win, remove_artifacts,...
+        minPeakThrMultiplier,...
+        maxPeakThrMultiplier,...
+        posPeakThrMultiplier);
+        
 elseif startsWith(wname, 'customAbs')
     multiplier = 0;
     [spikeTrain, ~, ~] = detectSpikesThreshold(trace, multiplier, ...