Update revision.jl to modify image and stimulus file paths, disable spike train analysis, and add functionality to save analysis figures for both raw data and ROI analysis, enhancing data processing and visualization capabilities.

Author: mattar13

test/revision.jl

@@ -10,21 +10,27 @@ using PhysiologyAnalysis
 
 
 # ╔═╡This task is for extraction of points, centroids, and ROIs using cellpose
-img_fn = raw"F:\Data\Two Photon\2025-05-02-GRAB-DA-nirCAT-STR\grab-nircat-str-kpuff_3x012.tif"
-stim_fn = raw"F:\Data\Patching\2025-05-02-GRAB-DA-STR\25502017.abf"
+#Kpuff looks really good
+
+# #We should look through the available files and see which ones fit
+# img_fn = raw"F:\Data\Two Photon\2025-05-02-GRAB-DA-nirCAT-STR\grab-nircat-str-20hz-100uA001.tif"
+# stim_fn = raw"F:\Data\Patching\2025-05-02-GRAB-DA-STR\25502000.abf"
+
+#Good but a big bubble
+# img_fn = raw"F:\Data\Two Photon\2025-05-02-GRAB-DA-nirCAT-STR\grab-nircat-str-3s_20hz_30uA_3x006.tif"
+# stim_fn = raw"F:\Data\Patching\2025-05-02-GRAB-DA-STR\25502007.abf"
 
-#We should look through the available files and see which ones fit
-img_fn = raw"F:\Data\Two Photon\2025-05-02-GRAB-DA-nirCAT-STR\grab-nircat-str-20hz-100uA001.tif"
-stim_fn = raw"F:\Data\Patching\2025-05-02-GRAB-DA-STR\25502000.abf"
+img_fn = raw"F:\Data\Two Photon\2025-05-02-GRAB-DA-nirCAT-STR\grab-nircat-str-kpuff011.tif"
+stim_fn = raw"F:\Data\Patching\2025-05-02-GRAB-DA-STR\25502015.abf"
 
-#We should look through the available files and see which ones fit
-img_fn = raw"F:\Data\Two Photon\2025-05-02-GRAB-DA-nirCAT-STR\grab-nircat-str-20hz-100uA001.tif"
-stim_fn = raw"F:\Data\Patching\2025-05-02-GRAB-DA-STR\25502000.abf"
+#%%
+img_fn = raw"F:\Data\Two Photon\2025-05-02-GRAB-DA-nirCAT-STR\grab-nircat-str-kpuff_3x012.tif"
+stim_fn = raw"F:\Data\Patching\2025-05-02-GRAB-DA-STR\25502017.abf"
 
 data2P = readImage(img_fn);
 deinterleave!(data2P) #This seperates the movies into two seperate movies
 
-spike_train = true
+spike_train = false
 if spike_train
     #If we have a electrical stimulus we need to do the spike train analysis
     addStimulus!(data2P, stim_fn, "IN 3", flatten_episodic = true, stimulus_threshold = 0.5)
@@ -35,6 +41,7 @@ else
     addStimulus!(data2P, stim_fn, "IN 2", flatten_episodic = true)
     time2P = data2P.t
 end
+getStimulusProtocol(data2P)
 
 # Split the image into 8x8 pixel ROIs
 pixel_splits_roi!(data2P, 8)
@@ -62,11 +69,18 @@ println("Found $(length(sig_rois)) significant ROIs")
 fit_params = get_fit_parameters(roi_analysis)
 println("Mean amplitude of significant ROIs: ", mean(first.(fit_params)))
 
-fig = plot_roi_analysis(data2P, stim_idx = 2)
-display(fig)
-
-
 #%% Test the new simple analysis plot function
 PhysiologyPlotting.__init__()
 fig_raw = PhysiologyPlotting.plot_analysis(data2P)
-display(fig_raw)
+# display(fig_raw)
+
+#%%
+# Save the raw analysis figure
+save(raw"F:\Data\Analysis\StriatumAnalysis\Potassium Puffs\fig_raw.png", fig_raw)
+
+#%%
+fig = plot_roi_analysis(data2P, stim_idx = 2)
+display(fig)
+
+# Save the ROI analysis figure
+save(raw"F:\Data\Analysis\StriatumAnalysis\Potassium Puffs\fig_roi_analysis.png", fig)