altered imzML parser to be compatible with timsconverter, small improvements on the UI, other small bug fixes done

README.md

@@ -22,7 +22,7 @@ https://codeberg.org/LabABI/JuliaMSI
    ~/Downloads/JuliaMSI-main/juliamsi
 2. Without entering the Julia environment, launch the project in your terminal with the following command (which works for all operating systems):
    ```
-   julia --project=. start_MSI_GUI.jl
+   julia --threads auto --project=. start_MSI_GUI.jl
    ```
 3. After the script has finished loading, you can open a [page](http://127.0.0.1:1481/) in your browser with the web app running.
 

app.jl

@@ -159,6 +159,14 @@ include("./julia_imzML_visual.jl")
     ## Plots
     # Local image to plot
     layoutImg=PlotlyBase.Layout(
+        title=PlotlyBase.attr(
+            text="",
+            font=PlotlyBase.attr(
+                family="Roboto, Lato, sans-serif",
+                size=14,
+                color="black"
+            )
+        ),
         xaxis=PlotlyBase.attr(
             visible=false,
             scaleanchor="y",
@@ -185,7 +193,14 @@ include("./julia_imzML_visual.jl")
     @out plotlayoutImgTComp=layoutImg
     # Interface Plot Spectrum
     layoutSpectra=PlotlyBase.Layout(
-        title="Spectrum plot",
+        title=PlotlyBase.attr(
+            text="Spectrum plot",
+            font=PlotlyBase.attr(
+                family="Roboto, Lato, sans-serif",
+                size=18,
+                color="black"
+            )
+        ),
         hovermode="closest",
         xaxis=PlotlyBase.attr(
             title="<i>m/z</i>",
@@ -215,7 +230,14 @@ include("./julia_imzML_visual.jl")
 
     # Interface Plot Surface
     layoutContour=PlotlyBase.Layout(
-        title="2D Topographic map",
+        title=PlotlyBase.attr(
+            text="2D Topographic map",
+            font=PlotlyBase.attr(
+                family="Roboto, Lato, sans-serif",
+                size=18,
+                color="black"
+            )
+        ),
         xaxis=PlotlyBase.attr(
             visible=false,
             scaleanchor="y"
@@ -226,7 +248,7 @@ include("./julia_imzML_visual.jl")
         margin=attr(l=0,r=0,t=100,b=0,pad=0)
     )
     # Dummy 2D surface plot
-    traceContour=PlotlyBase.scatter(x=Vector{Float64}(), y=Vector{Float64}(), mode="lines")
+    traceContour=PlotlyBase.contour(x=Vector{Float64}(), y=Vector{Float64}(), mode="lines")
     # Create conection to frontend
     @out plotdataC=[traceContour]
     @out plotlayoutC=layoutContour
@@ -234,7 +256,14 @@ include("./julia_imzML_visual.jl")
     # Interface Plot 3d
     # Define the layout for the 3D plot
     layout3D=PlotlyBase.Layout(
-        title="3D Surface plot",
+        title=PlotlyBase.attr(
+            text="3D Surface plot",
+            font=PlotlyBase.attr(
+                family="Roboto, Lato, sans-serif",
+                size=18,
+                color="black"
+            )
+        ),
         scene=attr(
             xaxis_title="X",
             yaxis_title="Y",
@@ -386,6 +415,43 @@ include("./julia_imzML_visual.jl")
                         # Use the new get_mz_slice with the centralized MSIData object
                         println("get_mz_slice time:")
                         slice = @time get_mz_slice(msi_data, Nmass, Tol)
+
+                        # Failsafe check for empty slice
+                        if all(iszero, slice)
+                            msg = "No intensity data found for m/z = $Nmass with tolerance = $Tol. The resulting image is black. Please consider using a larger tolerance."
+                            warning_msg = true
+                            
+                            # Generate a black image but skip the colorbar that would crash
+                            timestamp = string(time_ns())
+                            text_nmass = replace(string(Nmass), "." => "_")
+                            sliceQuant = zeros(UInt8, size(slice))
+                            
+                            if triqEnabled
+                                @time save_bitmap(joinpath("public", "TrIQ_$(text_nmass).bmp"), sliceQuant, ViridisPalette)
+                                imgIntT = "/TrIQ_$(text_nmass).bmp?t=$(timestamp)"
+                                plotdataImgT, plotlayoutImgT, imgWidth, imgHeight = loadImgPlot(imgIntT)
+                                current_triq = "TrIQ_$(text_nmass).bmp"
+                                msgtriq = "TrIQ image with the Nmass of $(replace(text_nmass, "_" => ".")) (No data)"
+                                colorbarT = "" # Clear colorbar
+                                current_col_triq = ""
+                                triq_bmp = sort(filter(filename -> startswith(filename, "TrIQ_") && endswith(filename, ".bmp"), readdir("public")), lt=natural)
+                                selectedTab = "tab1"
+                            else
+                                @time save_bitmap(joinpath("public", "MSI_$(text_nmass).bmp"), sliceQuant, ViridisPalette)
+                                imgInt = "/MSI_$(text_nmass).bmp?t=$(timestamp)"
+                                plotdataImg, plotlayoutImg, imgWidth, imgHeight = loadImgPlot(imgInt)
+                                current_msi = "MSI_$(text_nmass).bmp"
+                                msgimg = "Image with the Nmass of $(replace(text_nmass, "_" => ".")) (No data)"
+                                colorbar = "" # Clear colorbar
+                                current_col_msi = ""
+                                msi_bmp = sort(filter(filename -> startswith(filename, "MSI_") && endswith(filename, ".bmp"), readdir("public")), lt=natural)
+                                selectedTab = "tab0"
+                            end
+                            fTime = time()
+                            eTime = round(fTime - sTime, digits=3)
+                            # The warning message is already set above
+                        else
+                            # Original path for when data is found
                             fig = CairoMakie.Figure(size=(150, 250)) # Container
                             timestamp = string(time_ns())
 
@@ -399,7 +465,7 @@ include("./julia_imzML_visual.jl")
                                     if MFilterEnabled
                                         sliceTriq = round.(UInt8, median_filter(sliceTriq))
                                     end
-                                sliceTriq = reverse(sliceTriq, dims=2)
+
                                     println("save_bitmap time:")
                                     @time save_bitmap(joinpath("public", "TrIQ_$(text_nmass).bmp"), sliceTriq, ViridisPalette)
 
@@ -428,7 +494,7 @@ include("./julia_imzML_visual.jl")
                                 if MFilterEnabled
                                     sliceQuant = round.(UInt8, median_filter(sliceQuant))
                                 end
-                            sliceQuant = reverse(sliceQuant, dims=2)
+
                                 println("save_bitmap time:")
                                 @time save_bitmap(joinpath("public", "MSI_$(text_nmass).bmp"), sliceQuant, ViridisPalette)
 
@@ -450,6 +516,7 @@ include("./julia_imzML_visual.jl")
                                 eTime = round(fTime - sTime, digits=3)
                                 msg = "The image has been created in $(eTime) seconds successfully inside the 'public' folder of the app"
                             end
+                        end
                     catch e
                         msg = "There was an error creating the image: $e"
                         warning_msg = true
@@ -624,6 +691,7 @@ include("./julia_imzML_visual.jl")
         else
             traceImg=PlotlyBase.heatmap(x=Vector{Float64}(), y=Vector{Float64}())
             plotdataImg=[traceImg]
+            plotlayoutImg=layoutImg
             msgimg=""
         end
     end
@@ -651,6 +719,7 @@ include("./julia_imzML_visual.jl")
         else
             traceImg=PlotlyBase.heatmap(x=Vector{Float64}(), y=Vector{Float64}())
             plotdataImg=[traceImg]
+            plotlayoutImg=layoutImg
             msgimg=""
         end
     end
@@ -679,6 +748,7 @@ include("./julia_imzML_visual.jl")
         else
             traceImg=PlotlyBase.heatmap(x=Vector{Float64}(), y=Vector{Float64}())
             plotdataImgT=[traceImg]
+            plotlayoutImgT=layoutImg
             msgtriq=""
         end
     end
@@ -706,6 +776,7 @@ include("./julia_imzML_visual.jl")
         else
             traceImg=PlotlyBase.heatmap(x=Vector{Float64}(), y=Vector{Float64}())
             plotdataImgT=[traceImg]
+            plotlayoutImgT=layoutImg
             msgtriq=""
         end
     end
@@ -735,6 +806,7 @@ include("./julia_imzML_visual.jl")
         else
             traceImg=PlotlyBase.heatmap(x=Vector{Float64}(), y=Vector{Float64}())
             plotdataImgComp=[traceImg]
+            plotlayoutImgComp=layoutImg
             msgimgComp=""
         end
     end
@@ -763,6 +835,7 @@ include("./julia_imzML_visual.jl")
         else
             traceImg=PlotlyBase.heatmap(x=Vector{Float64}(), y=Vector{Float64}())
             plotdataImgComp=[traceImg]
+            plotlayoutImgComp=layoutImg
             msgimgComp=""
         end
     end
@@ -791,6 +864,7 @@ include("./julia_imzML_visual.jl")
         else
             traceImg=PlotlyBase.heatmap(x=Vector{Float64}(), y=Vector{Float64}())
             plotdataImgTComp=[traceImg]
+            plotlayoutImgTComp=layoutImg
             msgtriqComp=""
         end
     end
@@ -819,6 +893,7 @@ include("./julia_imzML_visual.jl")
         else
             traceImg=PlotlyBase.heatmap(x=Vector{Float64}(), y=Vector{Float64}())
             plotdataImgTComp=[traceImg]
+            plotlayoutImgTComp=layoutImg
             msgtriqComp=""
         end
     end
@@ -1026,9 +1101,20 @@ include("./julia_imzML_visual.jl")
     @onchange data_click begin
         if selectedTab == "tab1" || selectedTab == "tab0"
             # This is for the image heatmaps
-            cursor_data = data_click["cursor"]
+            cursor_data = get(data_click, "cursor", nothing)
-            x = Int32(round(cursor_data["x"]))
+            if cursor_data === nothing
-            y = Int32(round(cursor_data["y"])) # y is negative in the UI
+                return
+            end
+
+            x_val = get(cursor_data, "x", nothing)
+            y_val = get(cursor_data, "y", nothing)
+
+            if x_val === nothing || y_val === nothing
+                return # Do nothing if coordinates are not provided by the event
+            end
+
+            x = Int32(round(x_val))
+            y = Int32(round(y_val)) # y is negative in the UI
 
             # Update the reactive coordinates, which will trigger the crosshair update
             xCoord = clamp(x, 1, imgWidth)
@@ -1107,3 +1193,40 @@ end
 # Register a new route and the page that will be loaded on access
 @page("/", "app.jl.html")
 end
+
+#=
+function __init__()
+    @async begin
+        println("Pre-compiling functions at startup...")
+        
+        # Create a dummy MSIData object to be used for pre-compilation
+        dummy_source = ImzMLSource("dummy.ibd", Float32, Float32)
+        dummy_meta = MSI_src.SpectrumMetadata(0,0,"",MSI_src.UNKNOWN, MSI_src.SpectrumAsset(Float32,false,0,0,:mz), MSI_src.SpectrumAsset(Float32,false,0,0,:intensity))
+        dummy_msi_data = MSIData(dummy_source, [dummy_meta], (1,1), zeros(Int,1,1), 0)
+
+        # Pre-compile functions from btnSearch
+        try OpenMSIData("dummy.imzML") catch end
+        try precompute_analytics(dummy_msi_data) catch end
+
+        # Pre-compile functions from mainProcess
+        try get_mz_slice(dummy_msi_data, 1.0, 1.0) catch end
+        try TrIQ(zeros(10,10), 256, 0.98) catch end
+        try quantize_intensity(zeros(10,10), 256) catch end
+        
+        dummy_bmp_path = joinpath("public", "dummy.bmp")
+        dummy_png_path = joinpath("public", "dummy.png")
+        try 
+            save_bitmap(dummy_bmp_path, zeros(UInt8, 10, 10), ViridisPalette)
+            loadImgPlot("/dummy.bmp")
+            generate_colorbar_image(zeros(10,10), 256, dummy_png_path)
+        catch e
+            @warn "Pre-compilation step failed (this is expected if dummy files can't be created/read)"
+        finally
+            rm(dummy_bmp_path, force=true)
+            rm(dummy_png_path, force=true)
+        end
+
+        println("Pre-compilation finished.")
+    end
+end
+=#

app.jl.html

@@ -1,4 +1,3 @@
-<template>
 <header id="header">
     <img src="/css/LABI_logo.png" alt="Labi Logo Icon" id="imgLogo">
     <div>
@@ -12,7 +11,7 @@
   <div id="extDivStyle" class="row col-12 q-pa-xl">
     <div class="row col-6">
       <!-- Left DIV -->
-      <div id="intDivStyle" class="st-col col-12 st-module">
+      <div id="intDivStyle-left" class="st-col col-12 st-module">
         <h6>Search for the imzML or mzML file in your system</h6>
         <q-input standout="custom-standout" class="q-ma-sm cursor-pointer" v-model="full_route" readonly label="Select your imzML or mzML file" v-on:click="btnSearch=true">
             <template v-slot:append>
@@ -58,7 +57,7 @@
           <!-- Spectra Plot Manipulation -->
           <div class="col-6">
             <div class="st-col col-6 col-sm">
-              <q-btn-dropdown id="btnStyle" class="q-ma-sm" :loading="progressSpectraPlot" :disable="btnSpectraDisable"
+              <q-btn-dropdown class="q-ma-sm btn-style" :loading="progressSpectraPlot" :disable="btnSpectraDisable"
                 label="Generate Spectra" icon="play_arrow">
                 <template v-slot:loading>
                   <q-spinner-hourglass class="on-left" />
@@ -99,22 +98,22 @@
           </div>
         </div>
         <div class="row">
-          <q-btn id="btnStyle" :loading="progress" class="q-ma-sm" :disabled="btnStartDisable" icon="play_arrow"
+          <q-btn :loading="progress" class="q-ma-sm btn-style" :disabled="btnStartDisable" icon="play_arrow"
-            v-on:click="mainProcess=true" padding="lg" label="Main process">
+            v-on:click="mainProcess=true" padding="lg" label="Generate Spectra">
             <template v-slot:loading>
               <q-spinner-hourglass class="on-left" />
               Loading...
             </template>
           </q-btn>
-          <q-btn id="btnStyle" icon="zoom_out_map" class="q-ma-sm on-right" v-on:click="compareBtn=true" padding="sm"
+          <q-btn icon="zoom_out_map" class="q-ma-sm on-right btn-style" v-on:click="compareBtn=true" padding="sm"
             label="Compare"></q-btn>
-          <q-btn id="btnStyle" class="q-ma-sm" :disable="btnMetadataDisable"
+          <q-btn class="q-ma-sm btn-style" :disable="btnMetadataDisable"
             v-on:click="showMetadataBtn=true" label="Show Metadata"></q-btn>
         </div>
         <p>{{msg}}</p>
 
         <div class="row st-col col-12">
-          <q-btn-dropdown id="btnStyle" class="q-ma-sm" :loading="progressPlot" :disable="btnPlotDisable"
+          <q-btn-dropdown class="q-ma-sm btn-style" :loading="progressPlot" :disable="btnPlotDisable"
             label="Generate Plots" icon="play_arrow">
             <template v-slot:loading>
               <q-spinner-hourglass class="on-left" />
@@ -147,7 +146,7 @@
               </q-item>
             </q-list>
           </q-btn-dropdown>
-          <q-btn-dropdown id="btnStyle" icon="search" class="q-ma-sm" :disable="btnOpticalDisable"
+          <q-btn-dropdown icon="search" class="q-ma-sm btn-style" :disable="btnOpticalDisable"
             label="Load your optical image">
             <q-item clickable v-close-popup v-on:click="btnOptical=true">
               <q-item-section>
@@ -169,25 +168,25 @@
     </div>
     <div class="row col-6">
       <!-- Right DIV -->
-      <div id="intDivStyle" class="st-col col-12 col-sm st-module">
+      <div id="intDivStyle-right" class="st-col col-12 col-sm st-module">
-        <st-tabs id="tabHeader" :ids="tabIDs" :labels="tabLabels" v-model="selectedTab" no-arrows></st-tabs>
+        <st-tabs id="tabHeader-main" :ids="tabIDs" :labels="tabLabels" v-model="selectedTab" no-arrows></st-tabs>
         <q-tab-panels v-model="selectedTab">
           <q-tab-panel name="tab0">
             <!-- Content for Tab 0 -->
             <!-- Btn image changer -->
             <h6>Image visualizer</h6>
             <div>
-              <q-btn id="btnStyle" icon="arrow_back" class="q-my-sm" v-on:click="imgMinus=true"></q-btn>
+              <q-btn icon="arrow_back" class="q-my-sm btn-style" v-on:click="imgMinus=true"></q-btn>
-              <q-btn id="btnStyle" icon="arrow_forward" class="q-my-sm on-right" v-on:click="imgPlus=true"></q-btn>
+              <q-btn icon="arrow_forward" class="q-my-sm on-right btn-style" v-on:click="imgPlus=true"></q-btn>
             </div>
             <!-- Image manager -->
-            <div id="image-container" class="row st-col col-12">
+            <div id="image-container-normal" class="row st-col col-12">
               <div class="col-10 q-pa-none q-ma-none">
-                <plotly id="plotStyle" :data="plotdataImg" :layout="plotlayoutImg" class="q-pa-none q-ma-none sync_data"
+                <plotly id="plotImg" :data="plotdataImg" :layout="plotlayoutImg" class="q-pa-none q-ma-none sync_data"
                   @click="data_click"></plotly>
               </div>
               <div class="col-2 q-pa-none q-ma-none">
-                <q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbar"></q-img>
+                <q-img id="colorbar-normal" class="q-ma-none q-pa-none" :src="colorbar"></q-img>
               </div>
             </div>
             <p>{{msgimg}}</p>
@@ -198,17 +197,17 @@
             <!-- Triq Btn image changer -->
             <h6>TrIQ visualizer</h6>
             <div>
-              <q-btn id="btnStyle" icon="arrow_back" class="q-my-sm" v-on:click="imgMinusT=true"></q-btn>
+              <q-btn icon="arrow_back" class="q-my-sm btn-style" v-on:click="imgMinusT=true"></q-btn>
-              <q-btn id="btnStyle" icon="arrow_forward" class="q-my-sm on-right" v-on:click="imgPlusT=true"></q-btn>
+              <q-btn icon="arrow_forward" class="q-my-sm on-right btn-style" v-on:click="imgPlusT=true"></q-btn>
             </div>
             <!-- Triq Image manager -->
-            <div id="image-container" class="row st-col col-12">
+            <div id="image-container-triq" class="row st-col col-12">
               <div class="col-10 q-pa-none q-ma-none ">
-                <plotly id="plotStyle" :data="plotdataImgT" :layout="plotlayoutImgT"
+                <plotly id="plotImgT" :data="plotdataImgT" :layout="plotlayoutImgT"
                   class="q-pa-none q-ma-none sync_data" @click="data_click"></plotly>
               </div>
               <div class="col-2 q-pa-none q-ma-none ">
-                <q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbarT"></q-img>
+                <q-img id="colorbar-triq" class="q-ma-none q-pa-none" :src="colorbarT"></q-img>
               </div>
             </div>
             <p>{{msgtriq}}</p>
@@ -216,16 +215,16 @@
 
           <q-tab-panel name="tab2">
             <!-- Content for Tab 2 -->
-            <plotly id="plotStyle" :data="plotdata" :layout="plotlayout" class="q-pa-none q-ma-none"></plotly>
+            <plotly id="plotSpectra" :data="plotdata" :layout="plotlayout" class="q-pa-none q-ma-none"></plotly>
           </q-tab-panel>
 
           <q-tab-panel name="tab3">
             <!-- Content for Tab 3 -->
-            <plotly id="plotStyle" :data="plotdataC" :layout="plotlayoutC" class="q-pa-none q-ma-none"></plotly>
+            <plotly id="plotTopo" :data="plotdataC" :layout="plotlayoutC" class="q-pa-none q-ma-none"></plotly>
           </q-tab-panel>
           <q-tab-panel name="tab4">
             <!-- Content for Tab 4 -->
-            <plotly id="plotStyle3d" :data="plotdata3d" :layout="plotlayout3d" class="q-pa-none q-ma-none"></plotly>
+            <plotly id="plot3d" :data="plotdata3d" :layout="plotlayout3d" class="q-pa-none q-ma-none"></plotly>
           </q-tab-panel>
         </q-tab-panels>
       </div>
@@ -263,23 +262,23 @@
       <q-card-section class="q-pt-none col-12">
         <div class="row">
           <div class="col-6">
-            <st-tabs id="tabHeader" :ids="tabIDs" :labels="tabLabels" v-model="selectedTab"></st-tabs>
+            <st-tabs id="tabHeaderCompareLeft" :ids="tabIDs" :labels="tabLabels" v-model="selectedTab"></st-tabs>
             <q-tab-panels v-model="selectedTab">
               <q-tab-panel name="tab0">
                 <!-- Content for Tab 0 -->
                 <!-- Btn image changer -->
                 <div>
-                  <q-btn id="btnStyle" icon="arrow_back" class="q-my-sm" v-on:click="imgMinus=true"></q-btn>
+                  <q-btn icon="arrow_back" class="q-my-sm btn-style" v-on:click="imgMinus=true"></q-btn>
-                  <q-btn id="btnStyle" icon="arrow_forward" class="q-my-sm on-right" v-on:click="imgPlus=true"></q-btn>
+                  <q-btn icon="arrow_forward" class="q-my-sm on-right btn-style" v-on:click="imgPlus=true"></q-btn>
                 </div>
                 <!-- Image manager -->
-                <div id="image-container" class="row st-col col-12">
+                <div id="image-container-compare-left-normal" class="row st-col col-12">
                   <div class="col-10 q-pa-none q-ma-none ">
-                    <plotly id="plotStyle" :data="plotdataImg" :layout="plotlayoutImg" class="q-pa-none q-ma-none">
+                    <plotly id="plotImgCompareLeft" :data="plotdataImg" :layout="plotlayoutImg" class="q-pa-none q-ma-none">
                     </plotly>
                   </div>
                   <div class="col-2">
-                    <q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbar"></q-img>
+                    <q-img id="colorbarCompareLeft" class="q-ma-none q-pa-none" :src="colorbar"></q-img>
                   </div>
                 </div>
                 <p>{{msgimg}}</p>
@@ -289,56 +288,56 @@
                 <!-- Content for Tab 1 -->
                 <!-- Triq Btn image changer -->
                 <div>
-                  <q-btn id="btnStyle" icon="arrow_back" class="q-my-sm" v-on:click="imgMinusT=true"></q-btn>
+                  <q-btn icon="arrow_back" class="q-my-sm btn-style" v-on:click="imgMinusT=true"></q-btn>
-                  <q-btn id="btnStyle" icon="arrow_forward" class="q-my-sm on-right" v-on:click="imgPlusT=true"></q-btn>
+                  <q-btn icon="arrow_forward" class="q-my-sm on-right btn-style" v-on:click="imgPlusT=true"></q-btn>
                 </div>
                 <!-- Triq Image manager -->
-                <div id="image-container" class="row st-col col-12">
+                <div id="image-container-compare-left-triq" class="row st-col col-12">
                   <div class="col-10 q-pa-none q-ma-none ">
-                    <plotly id="plotStyle" :data="plotdataImgT" :layout="plotlayoutImgT" class="q-pa-none q-ma-none">
+                    <plotly id="plotImgTCompareLeft" :data="plotdataImgT" :layout="plotlayoutImgT" class="q-pa-none q-ma-none">
                     </plotly>
                   </div>
                   <div class="col-2">
-                    <q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbarT"></q-img>
+                    <q-img id="colorbarTCompareLeft" class="q-ma-none q-pa-none" :src="colorbarT"></q-img>
                   </div>
                 </div>
                 <p>{{msgtriq}}</p>
               </q-tab-panel>
               <q-tab-panel name="tab2">
                 <!-- Content for Tab 2 -->
-                <plotly id="plotStyle" :data="plotdata" :layout="plotlayout" class="q-pa-none q-ma-none"></plotly>
+                <plotly id="plotSpectraCompareLeft" :data="plotdata" :layout="plotlayout" class="q-pa-none q-ma-none"></plotly>
               </q-tab-panel>
               <q-tab-panel name="tab3">
                 <!-- Content for Tab 3 -->
-                <plotly id="plotStyle" :data="plotdataC" :layout="plotlayoutC" class="q-pa-none q-ma-none"></plotly>
+                <plotly id="plotTopoCompareLeft" :data="plotdataC" :layout="plotlayoutC" class="q-pa-none q-ma-none"></plotly>
               </q-tab-panel>
               <q-tab-panel name="tab4">
                 <!-- Content for Tab 4 -->
-                <plotly id="plotStyle3d" :data="plotdata3d" :layout="plotlayout3d" class="q-pa-none q-ma-none"></plotly>
+                <plotly id="plot3dCompareLeft" :data="plotdata3d" :layout="plotlayout3d" class="q-pa-none q-ma-none"></plotly>
               </q-tab-panel>
             </q-tab-panels>
           </div>
           <div class="col-6">
-            <st-tabs id="tabHeader" :ids="CompTabIDs" :labels="CompTabLabels" v-model="CompSelectedTab" outside-arrows
+            <st-tabs id="tabHeaderCompareRight" :ids="CompTabIDs" :labels="CompTabLabels" v-model="CompSelectedTab" outside-arrows
               mobile-arrows></st-tabs>
             <q-tab-panels v-model="CompSelectedTab">
               <q-tab-panel name="tab0">
                 <!-- Content for Tab 0 -->
                 <!-- Btn image changer -->
                 <div>
-                  <q-btn id="btnStyle" icon="arrow_back" class="q-my-sm" v-on:click="imgMinusComp=true"></q-btn>
+                  <q-btn icon="arrow_back" class="q-my-sm btn-style" v-on:click="imgMinusComp=true"></q-btn>
-                  <q-btn id="btnStyle" icon="arrow_forward" class="q-my-sm on-right"
+                  <q-btn icon="arrow_forward" class="q-my-sm on-right btn-style"
                     v-on:click="imgPlusComp=true"></q-btn>
                 </div>
                 <!-- Image manager -->
-                <div id="image-container" class="row st-col col-12">
+                <div id="image-container-compare-right-normal" class="row st-col col-12">
                   <div class="col-10 q-pa-none q-ma-none ">
-                    <plotly id="plotStyle" :data="plotdataImgComp" :layout="plotlayoutImgComp"
+                    <plotly id="plotImgCompareRight" :data="plotdataImgComp" :layout="plotlayoutImgComp"
                       class="q-pa-none q-ma-none">
                     </plotly>
                   </div>
                   <div class="col-2 q-pa-none q-ma-none ">
-                    <q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbarComp"></q-img>
+                    <q-img id="colorbarComp" class="q-ma-none q-pa-none" :src="colorbarComp"></q-img>
                   </div>
                 </div>
                 <p>{{msgimgComp}}</p>
@@ -348,34 +347,34 @@
                 <!-- Content for Tab 1 -->
                 <!-- Triq Btn image changer -->
                 <div>
-                  <q-btn id="btnStyle" icon="arrow_back" class="q-my-sm" v-on:click="imgMinusTComp=true"></q-btn>
+                  <q-btn icon="arrow_back" class="q-my-sm btn-style" v-on:click="imgMinusTComp=true"></q-btn>
-                  <q-btn id="btnStyle" icon="arrow_forward" class="q-my-sm on-right"
+                  <q-btn icon="arrow_forward" class="q-my-sm on-right btn-style"
                     v-on:click="imgPlusTComp=true"></q-btn>
                 </div>
                 <!-- Triq Image manager -->
-                <div id="image-container" class="row st-col col-12">
+                <div id="image-container-compare-right-triq" class="row st-col col-12">
                   <div class="col-10 q-pa-none q-ma-none ">
-                    <plotly id="plotStyle" :data="plotdataImgTComp" :layout="plotlayoutImgTComp"
+                    <plotly id="plotImgTCompareRight" :data="plotdataImgTComp" :layout="plotlayoutImgTComp"
                       class="q-pa-none q-ma-none">
                     </plotly>
                   </div>
                   <div class="col-2 q-pa-none q-ma-none ">
-                    <q-img id="colorbar" class="q-ma-none q-pa-none" :src="colorbarTComp"></q-img>
+                    <q-img id="colorbarTComp" class="q-ma-none q-pa-none" :src="colorbarTComp"></q-img>
                   </div>
                 </div>
                 <p>{{msgtriqComp}}</p>
               </q-tab-panel>
               <q-tab-panel name="tab2">
                 <!-- Content for Tab 2 -->
-                <plotly id="plotStyle" :data="plotdata" :layout="plotlayout" class="q-pa-none q-ma-none"></plotly>
+                <plotly id="plotSpectraCompareRight" :data="plotdata" :layout="plotlayout" class="q-pa-none q-ma-none"></plotly>
               </q-tab-panel>
               <q-tab-panel name="tab3">
                 <!-- Content for Tab 3 -->
-                <plotly id="plotStyle" :data="plotdataC" :layout="plotlayoutC" class="q-pa-none q-ma-none"></plotly>
+                <plotly id="plotTopoCompareRight" :data="plotdataC" :layout="plotlayoutC" class="q-pa-none q-ma-none"></plotly>
               </q-tab-panel>
               <q-tab-panel name="tab4">
                 <!-- Content for Tab 4 -->
-                <plotly id="plotStyle3d" :data="plotdata3d" :layout="plotlayout3d" class="q-pa-none q-ma-none"></plotly>
+                <plotly id="plot3dCompareRight" :data="plotdata3d" :layout="plotlayout3d" class="q-pa-none q-ma-none"></plotly>
               </q-tab-panel>
             </q-tab-panels>
           </div>
@@ -412,5 +411,3 @@
         </q-card-actions>
     </q-card>
   </q-dialog>
-
-</template>

julia_imzML_visual.jl

@@ -26,6 +26,26 @@ function decrement_image(current_image, image_list)
 end
 
 ## Plot Image functions
+# Downsample an image matrix to a maximum dimension while preserving aspect ratio
+function downsample_image(img_matrix, max_dim::Int)
+    h, w = size(img_matrix)
+    if h <= max_dim && w <= max_dim
+        return img_matrix # No downsampling needed
+    end
+
+    aspect_ratio = w / h
+    if w > h
+        new_w = max_dim
+        new_h = round(Int, max_dim / aspect_ratio)
+    else
+        new_h = max_dim
+        new_w = round(Int, max_dim * aspect_ratio)
+    end
+
+    # imresize from Images.jl is perfect for this
+    return imresize(img_matrix, (new_h, new_w))
+end
+
 # loadImgPlot recieves the local directory of the image as a string,
 # returns the layout and data for the heatmap plotly plot
 # this function loads the image into a plot
@@ -46,6 +66,14 @@ function loadImgPlot(interfaceImg::String)
 
     # Create the layout
     layout=PlotlyBase.Layout(
+        title=PlotlyBase.attr(
+            text="",
+            font=PlotlyBase.attr(
+                family="Roboto, Lato, sans-serif",
+                size=14,
+                color="black"
+            )
+        ),
         xaxis=PlotlyBase.attr(
             visible=false,
             scaleanchor="y",
@@ -64,6 +92,7 @@ function loadImgPlot(interfaceImg::String)
         x=X,
         y=-Y,
         name="",
+        hoverinfo="x+y",
         showlegend=false,
         colorscale="Viridis",
         showscale=false,
@@ -110,6 +139,14 @@ function loadImgPlot(interfaceImg::String, overlayImg::String, imgTrans::Float64
 
     # Create the layout with overlay image
     layoutImg = PlotlyBase.Layout(
+        title=PlotlyBase.attr(
+            text="",
+            font=PlotlyBase.attr(
+                family="Roboto, Lato, sans-serif",
+                size=14,
+                color="black"
+            )
+        ),
         images = [attr(
             source = "$(overlayImg)?t=$(timestamp)",
             xref = "x",
@@ -140,6 +177,7 @@ function loadImgPlot(interfaceImg::String, overlayImg::String, imgTrans::Float64
         x = X,
         y = -Y,
         name = "",
+        hoverinfo = "x+y",
         showlegend = false,
         colorscale = "Viridis",
         showscale = false
@@ -169,6 +207,10 @@ function loadContourPlot(interfaceImg::String)
     kernel=Kernel.gaussian(sigma)
     elevation_smoothed=imfilter(elevation, kernel)
 
+    # --- DOWNSAMPLING FOR PERFORMANCE ---
+    elevation_smoothed = downsample_image(elevation_smoothed, 512)
+    # ---
+    
     # Create the X, Y meshgrid coordinates
     x=1:size(elevation_smoothed, 2)
     y=1:size(elevation_smoothed, 1)
@@ -182,7 +224,14 @@ function loadContourPlot(interfaceImg::String)
     tickT = log_tick_formatter(collect(tickV))
                 
     layout=PlotlyBase.Layout(
-        title="2D topographic map of $cleaned_img",
+        title=PlotlyBase.attr(
+            text="2D topographic map of $cleaned_img (downsampled)",
+            font=PlotlyBase.attr(
+                family="Roboto, Lato, sans-serif",
+                size=18,
+                color="black"
+            )
+        ),
         xaxis=PlotlyBase.attr(
             visible=false,
             scaleanchor="y"
@@ -228,6 +277,10 @@ function loadSurfacePlot(interfaceImg::String)
     kernel=Kernel.gaussian(sigma)
     elevation_smoothed=imfilter(elevation, kernel)
 
+    # --- DOWNSAMPLING FOR PERFORMANCE ---
+    elevation_smoothed = downsample_image(elevation_smoothed, 256)
+    # ---
+    
     # Create the X, Y meshgrid coordinates 
     x=1:size(elevation_smoothed, 2) 
     y=1:size(elevation_smoothed, 1)
@@ -247,7 +300,14 @@ function loadSurfacePlot(interfaceImg::String)
     aspect_ratio=attr(x=1, y=length(y) / length(x), z=0.5)
     # Define the layout for the 3D plot
     layout3D=PlotlyBase.Layout(
-        title="3D surface plot of $cleaned_img",
+        title=PlotlyBase.attr(
+            text="3D surface plot of $cleaned_img (downsampled)",
+            font=PlotlyBase.attr(
+                family="Roboto, Lato, sans-serif",
+                size=18,
+                color="black"
+            )
+        ),
         scene=attr(
             xaxis_nticks=x_nticks,
             yaxis_nticks=y_nticks,
@@ -377,8 +437,9 @@ function generate_colorbar_image(slice_data::AbstractMatrix, color_levels::Int,
     # 3. Create and save the colorbar image
     fig = Figure(size=(150, 250))
     Colorbar(fig[1, 1], 
-        colormap=cgrad(:viridis, bins),
+        colormap=cgrad(:viridis, bins, categorical=true),
-        limits=(min_val, max_val),
+        # limits=(min_val, max_val),
+        limits=(levels[1], levels[end]),
         label=(scale == 1 ? "Intensity" : "Intensity ×10^$(round(Int, 3 * exponent))"),
         ticks=(tick_positions, tick_labels),
         labelsize=20,
@@ -393,7 +454,14 @@ end
 # its values in the spectrum plot
 function meanSpectrumPlot(data::MSIData)
     layout = PlotlyBase.Layout(
-        title="Average Spectrum Plot",
+        title=PlotlyBase.attr(
+            text="Average Spectrum Plot",
+            font=PlotlyBase.attr(
+                family="Roboto, Lato, sans-serif",
+                size=18,
+                color="black"
+            )
+        ),
         hovermode="closest",
         xaxis=PlotlyBase.attr(
             title="<i>m/z</i>",
@@ -434,7 +502,7 @@ function xySpectrumPlot(data::MSIData, xCoord::Int, yCoord::Int, imgWidth::Int,
         x = clamp(xCoord, 1, imgWidth)
         y = clamp(yCoord, 1, imgHeight)
         
-        mz, intensity = GetSpectrum(data, x, y)
+        mz, intensity = GetSpectrum(data, Int(x), Int(y))
         plot_title = "Spectrum at ($x, $y)"
     else
         # For non-imaging data, treat xCoord as the spectrum index
@@ -445,7 +513,14 @@ function xySpectrumPlot(data::MSIData, xCoord::Int, yCoord::Int, imgWidth::Int,
     end
 
     layout = PlotlyBase.Layout(
-        title=plot_title,
+        title=PlotlyBase.attr(
+            text=plot_title,
+            font=PlotlyBase.attr(
+                family="Roboto, Lato, sans-serif",
+                size=18,
+                color="black"
+            )
+        ),
         hovermode="closest",
         xaxis=PlotlyBase.attr(
             title="<i>m/z</i>",
@@ -472,7 +547,14 @@ end
 
 function sumSpectrumPlot(data::MSIData)
     layout = PlotlyBase.Layout(
-        title="Total Spectrum Plot",
+        title=PlotlyBase.attr(
+            text="Total Spectrum Plot",
+            font=PlotlyBase.attr(
+                family="Roboto, Lato, sans-serif",
+                size=18,
+                color="black"
+            )
+        ),
         hovermode="closest",
         xaxis=PlotlyBase.attr(
             title="<i>m/z</i>",

public/css/genieapp.css

@@ -1,11 +1,11 @@
-#btnStyle {
+.btn-style {
-    background: #009f90;
+    background: #009f90 !important;
-    color: rgb(229, 236, 246);
+    color: rgb(229, 236, 246) !important;
     transition: background-color 0.3s ease;
 }
 
-#btnStyle:hover {
+.btn-style:hover {
-    background-color: #007f72;
+    background-color: #007f72 !important;
 }
 
 #imgInt {

src/MSIData.jl

@@ -61,6 +61,8 @@ struct SpectrumAsset
     axis_type::Symbol
 end
 
+@enum SpectrumMode CENTROID=1 PROFILE=2 UNKNOWN=3
+
 """
     SpectrumMetadata
 
@@ -69,6 +71,7 @@ Contains all metadata for a single spectrum, common to both imzML and mzML forma
 # Fields
 - `x`, `y`: The spatial coordinates of the spectrum (for imzML only).
 - `id`: The unique identifier string for the spectrum (for mzML only).
+- `mode`: The spectrum mode (`CENTROID` or `PROFILE`).
 - `mz_asset`: A `SpectrumAsset` for the m/z array.
 - `int_asset`: A `SpectrumAsset` for the intensity array.
 """
@@ -80,6 +83,7 @@ struct SpectrumMetadata
     # For mzML
     id::String
 
+    mode::SpectrumMode
     # Common binary data info
     mz_asset::SpectrumAsset
     int_asset::SpectrumAsset
@@ -345,25 +349,28 @@ as they can use this cached data. This function modifies the `MSIData` object in
 and is idempotent.
 """
 function precompute_analytics(msi_data::MSIData)
-    # Idempotency check: If already computed, do nothing.
+    # Idempotency check
     if msi_data.spectrum_stats_df !== nothing && hasproperty(msi_data.spectrum_stats_df, :MinMZ)
         println("Analytics have already been pre-computed.")
         return
     end
-    """
-    meta = msi_data.spectra_metadata[1]
-    println("First spectrum:")
-    println("  mz compressed: $(meta.mz_asset.is_compressed)")
-    println("  int compressed: $(meta.int_asset.is_compressed)")
-    println("  mz encoded_length: $(meta.mz_asset.encoded_length)")
-    println("  int encoded_length: $(meta.int_asset.encoded_length)")
     
     println("Pre-computing analytics (single pass)...")
-    """
     start_time = time_ns()
 
     num_spectra = length(msi_data.spectra_metadata)
     
+    # DEBUG: Check the first spectrum's metadata
+    if num_spectra > 0
+        first_meta = msi_data.spectra_metadata[1]
+        println("DEBUG First spectrum metadata:")
+        println("  mz_asset: format=$(first_meta.mz_asset.format), compressed=$(first_meta.mz_asset.is_compressed)")
+        println("  mz_asset: offset=$(first_meta.mz_asset.offset), encoded_length=$(first_meta.mz_asset.encoded_length)")
+        println("  int_asset: format=$(first_meta.int_asset.format), compressed=$(first_meta.int_asset.is_compressed)")
+        println("  int_asset: offset=$(first_meta.int_asset.offset), encoded_length=$(first_meta.int_asset.encoded_length)")
+        println("  mode: $(first_meta.mode)")
+    end
+
     # Initialize variables for global stats
     g_min_mz = Inf
     g_max_mz = -Inf
@@ -375,9 +382,21 @@ function precompute_analytics(msi_data::MSIData)
     num_points = Vector{Int}(undef, num_spectra)
     min_mzs = Vector{Float64}(undef, num_spectra)
     max_mzs = Vector{Float64}(undef, num_spectra)
+    modes = Vector{SpectrumMode}(undef, num_spectra)
+    is_compressed = Vector{Bool}(undef, num_spectra)
+
+    # DEBUG: Add counter to see how many spectra have data
+    spectra_with_data = 0
+    empty_spectra = 0
 
     _iterate_spectra_fast(msi_data) do idx, mz, intensity
+        # Store metadata
+        modes[idx] = msi_data.spectra_metadata[idx].mode
+        is_compressed[idx] = msi_data.spectra_metadata[idx].mz_asset.is_compressed || 
+                            msi_data.spectra_metadata[idx].int_asset.is_compressed
+        
         if isempty(mz)
+            empty_spectra += 1
             tics[idx] = 0.0
             bpis[idx] = 0.0
             bp_mzs[idx] = 0.0
@@ -385,6 +404,8 @@ function precompute_analytics(msi_data::MSIData)
             min_mzs[idx] = Inf
             max_mzs[idx] = -Inf
             return
+        else
+            spectra_with_data += 1
         end
 
         # Update global m/z range
@@ -402,6 +423,27 @@ function precompute_analytics(msi_data::MSIData)
         num_points[idx] = length(mz)
     end
 
+    # Add mode statistics
+    centroid_count = count(==(CENTROID), modes)
+    profile_count = count(==(PROFILE), modes)
+    unknown_count = count(==(UNKNOWN), modes)
+    
+    println("DEBUG Mode Statistics:")
+    println("  Centroid spectra: $centroid_count")
+    println("  Profile spectra: $profile_count")
+    println("  Unknown mode: $unknown_count")
+
+    # DEBUG: Print summary
+    println("DEBUG Analytics Summary:")
+    println("  Total spectra: $num_spectra")
+    println("  Spectra with data: $spectra_with_data")
+    println("  Empty spectra: $empty_spectra")
+    println("  Global m/z range: [$g_min_mz, $g_max_mz]")
+    println("  Centroid spectra: $(count(==(CENTROID), modes))")
+    println("  Profile spectra: $(count(==(PROFILE), modes))")
+    println("  Compressed spectra: $(sum(is_compressed))")
+    println("  Average points per spectrum: $(mean(num_points))")
+
     # Populate the MSIData object
     msi_data.global_min_mz = g_min_mz
     msi_data.global_max_mz = g_max_mz
@@ -412,7 +454,9 @@ function precompute_analytics(msi_data::MSIData)
         BasePeakMZ = bp_mzs,
         NumPoints = num_points,
         MinMZ = min_mzs,
-        MaxMZ = max_mzs
+        MaxMZ = max_mzs,
+        Mode = modes,
+        IsCompressed = is_compressed
     )
     
     duration = (time_ns() - start_time) / 1e9
@@ -731,12 +775,15 @@ function read_compressed_array(io::IO, asset::SpectrumAsset, format::Type)
     seek(io, asset.offset)
     
     if asset.is_compressed
-        # Read compressed bytes
+        # Read compressed bytes - use encoded_length as the number of compressed bytes
         compressed_bytes = read(io, asset.encoded_length)
         
+        println("DEBUG: Decompressing data - offset=$(asset.offset), compressed_bytes=$(length(compressed_bytes))")
+        
         local decompressed_bytes
         try
             decompressed_bytes = Libz.inflate(compressed_bytes)
+            println("DEBUG: Decompression successful - decompressed_bytes=$(length(decompressed_bytes))")
         catch e
             @error "ZLIB DECOMPRESSION FAILED. This is likely due to an incorrect offset or corrupt data in the .ibd file."
             @error "Asset offset: $(asset.offset), Encoded length: $(asset.encoded_length)"
@@ -747,8 +794,7 @@ function read_compressed_array(io::IO, asset::SpectrumAsset, format::Type)
             rethrow(e)
         end
         
-        # Use an IOBuffer to safely read the data, avoiding reinterpret errors
+        # Use an IOBuffer to safely read the data
-        # if the decompressed size is not a perfect multiple of the element size.
         bytes_io = IOBuffer(decompressed_bytes)
         n_elements = bytes_io.size ÷ sizeof(format)
         array = Array{format}(undef, n_elements)

src/ParserHelpers.jl

@@ -20,6 +20,7 @@ mutable struct SpecDim
     Packed::Bool
     Axis::Int
     Skip::Int
+    Mode::SpectrumMode
 end
 
 """
@@ -51,7 +52,7 @@ Retrieves an attribute's value from an XML tag string.
 """
 function get_attribute(source::AbstractString, tag::String = "([^=]+)")
     # Construct the regex pattern string
-    pattern_str = "\\s" * tag * "=\"([^\"]*)\""
+    pattern_str = "\\s*" * tag * "=\"([^\"]*)\""
     regStr = Regex(pattern_str)
     return match(regStr, source)
 end
@@ -70,18 +71,19 @@ compression status (`zlib`), and axis type (m/z vs. intensity).
 - A `SpecDim` struct populated with the parsed configuration.
 """
 function configure_spec_dim(stream)
-    axis = SpecDim(Float64, false, 1, 0)
+    axis = SpecDim(Float64, false, 1, 0, UNKNOWN)  # Add UNKNOWN as default mode
-    offset = position(stream)
     
     while !eof(stream)
         currLine = readline(stream)
         matchInfo = match(r"^\s*<(cvParam)", currLine)
 
         if matchInfo === nothing
-            matchInfo = match(r"^\s*", currLine)
+            # Check for end of cvParam block
-            axis.Skip = position(stream) - offset - length(currLine) + length(matchInfo.match)
+            if match(r"^\s*</", currLine) !== nothing
                 return axis
             end
+            continue
+        end
 
         index = length(matchInfo.captures[1])
         attr_match = get_attribute(currLine[index:end], "accession")
@@ -98,10 +100,14 @@ function configure_spec_dim(stream)
                 axis.Format = Int64
             elseif accession == "MS:1000574"   # zlib compression
                 axis.Packed = true
+            elseif accession == "MS:1000127"   # centroid spectrum
+                axis.Mode = CENTROID
+            elseif accession == "MS:1000128"   # profile spectrum  
+                axis.Mode = PROFILE
             end
         end
     end
-    return axis # Should be unreachable if file is well-formed
+    return axis
 end
 
 # ============================================================================

src/imzML.jl

@@ -26,16 +26,25 @@ Core Functions:
 Determines the storage order of the m/z and intensity arrays.
 """
 function axes_config_img(stream)
-    tag = find_tag(stream, r"^\s*<(referenceableParamGroup )")
+    param_groups = Dict{String, SpecDim}()
-    value = get_attribute(tag.captures[1], "intensityArray")
+    find_tag(stream, r"<referenceableParamGroupList")
-    order = 1 + (value !== nothing)
 
-    axis = Array{SpecDim,1}(undef, 2)
+    while true
-    axis[order] = configure_spec_dim(stream)
+        pos = position(stream)
+        line = readline(stream)
 
-    find_tag(stream, r"^\s*<(referenceableParamGroup )")
+        if eof(stream) || occursin("</referenceableParamGroupList>", line)
-    axis[xor(order, 3)] = configure_spec_dim(stream)
+            break
-    return axis
+        end
+
+        id_match = match(r"<referenceableParamGroup id=\"([^\"]+)\"", line)
+        if id_match !== nothing
+            id = id_match.captures[1]
+            spec_dim = configure_spec_dim(stream)
+            param_groups[id] = spec_dim
+        end
+    end
+    return param_groups
 end
 
 """
@@ -137,13 +146,57 @@ function get_spectrum_attributes(stream, hIbd)
     return skip
 end
 
+function determine_parser(stream, mz_is_compressed, int_is_compressed)
+    start_pos = position(stream)
+    spectrum_xml = ""
     
-"""
+    try
-    load_imzml_lazy(file_path::String; cache_size=100)
+        # Find the start of the first spectrum tag
+        while !eof(stream)
+            line = readline(stream)
+            if occursin("<spectrum ", line)
+                spectrum_buffer = IOBuffer()
+                write(spectrum_buffer, line)
+                # Read until the end of the spectrum tag
+                while !eof(stream)
+                    line = readline(stream)
+                    write(spectrum_buffer, line)
+                    if occursin("</spectrum>", line)
+                        break
+                    end
+                end
+                spectrum_xml = String(take!(spectrum_buffer))
+                break # Found the first spectrum, so we can stop
+            end
+        end
+    finally
+        seek(stream, start_pos) # Always reset stream position
+    end
+
+    if isempty(spectrum_xml)
+        # Fallback based on compression flags if no spectrum tag found
+        return (mz_is_compressed || int_is_compressed) ? :compressed : :uncompressed
+    end
+
+    # Inspect the XML content
+    has_neofx_markers = occursin("encodedLength=\"0\"", spectrum_xml) &&
+                        occursin("external encoded length", spectrum_xml)
+    
+    has_external_data_markers = occursin("IMS:1000101", spectrum_xml) && 
+                                occursin("IMS:1000102", spectrum_xml) &&
+                                occursin("IMS:1000103", spectrum_xml)
+
+    if has_neofx_markers
+        return :neofx
+    end
+    
+    if mz_is_compressed || int_is_compressed || has_external_data_markers
+        return :compressed
+    end
+
+    return :uncompressed
+end
 
-Main function to parse an `.imzML`/.ibd file pair and prepare for lazy loading.
-It now returns a unified MSIData object.
-"""
 function load_imzml_lazy(file_path::String; cache_size=100)
     println("DEBUG: Checking for .imzML file at $file_path")
     if !isfile(file_path)
@@ -162,22 +215,96 @@ function load_imzml_lazy(file_path::String; cache_size=100)
 
     try
         println("DEBUG: Configuring axes...")
-        axis = axes_config_img(stream)
+        param_groups = axes_config_img(stream)
         println("DEBUG: Getting image dimensions...")
         imgDim = get_img_dimensions(stream)
         width, height, num_spectra = imgDim
         println("DEBUG: Image dimensions: $(width)x$(height), $num_spectra spectra.")
 
-        mz_config_idx = findfirst(a -> a.Axis == 1, axis)
+        # Extract default formats from the parsed param_groups
-        int_config_idx = findfirst(a -> a.Axis == 2, axis)
+        mz_group = nothing
-        mz_format = axis[mz_config_idx].Format
+        int_group = nothing
-        intensity_format = axis[int_config_idx].Format
-        mz_is_compressed = axis[mz_config_idx].Packed
-        int_is_compressed = axis[int_config_idx].Packed
-        println("DEBUG: m/z format: $mz_format, Intensity format: $intensity_format")
-        println("DEBUG: m/z compressed: $mz_is_compressed, Intensity compressed: $int_is_compressed")
 
-        # --- NEW PARSING LOGIC based on the old, working code ---
+        for group in values(param_groups)
+            if group.Axis == 1
+                mz_group = group
+            elseif group.Axis == 2
+                int_group = group
+            end
+        end
+
+        if mz_group === nothing || int_group === nothing
+            @warn "Could not find global definitions for m/z and intensity arrays. Using hardcoded defaults (Float64)."
+            default_mz_format = Float64
+            default_intensity_format = Float64
+            mz_is_compressed = false
+            int_is_compressed = false
+            global_mode = UNKNOWN
+        else
+            default_mz_format = mz_group.Format
+            default_intensity_format = int_group.Format
+            mz_is_compressed = mz_group.Packed
+            int_is_compressed = int_group.Packed
+            global_mode = mz_group.Mode != UNKNOWN ? mz_group.Mode : int_group.Mode
+        end
+
+        println("DEBUG: m/z format: $default_mz_format, Intensity format: $default_intensity_format")
+        println("DEBUG: m/z compressed: $mz_is_compressed, Intensity compressed: $int_is_compressed")
+        println("DEBUG: Global mode: $global_mode")
+
+        # --- Parser Selection ---
+        parser_type = determine_parser(stream, mz_is_compressed, int_is_compressed)
+        println("DEBUG: Selected parser: $parser_type")
+
+        local spectra_metadata
+        if parser_type == :neofx
+            println("DEBUG: Using neofx parser.")
+            spectra_metadata = parse_neofx(stream, hIbd, param_groups, width, height, num_spectra, 
+                                           default_mz_format, default_intensity_format, 
+                                           mz_is_compressed, int_is_compressed, global_mode)
+        elseif parser_type == :compressed
+            println("DEBUG: Using compressed parser.")
+            spectra_metadata = parse_compressed(stream, hIbd, param_groups, width, height, num_spectra,
+                                           default_mz_format, default_intensity_format,
+                                           mz_is_compressed, int_is_compressed, global_mode)
+        else # :uncompressed
+            println("DEBUG: Using uncompressed parser.")
+            spectra_metadata = parse_uncompressed(stream, hIbd, param_groups, width, height, num_spectra,
+                                           default_mz_format, default_intensity_format,
+                                           mz_is_compressed, int_is_compressed, global_mode)
+        end
+
+        println("DEBUG: Metadata parsing complete.")
+        
+        # Build coordinate map for imzML files
+        println("DEBUG: Building coordinate map...")
+        coordinate_map = zeros(Int, width, height)
+        for (idx, meta) in enumerate(spectra_metadata)
+            if idx == 1
+                println("DIAGNOSTIC_WRITE: For index 1, attempting to write to coordinate_map[$(meta.x), $(meta.y)]")
+            end
+            if 1 <= meta.x <= width && 1 <= meta.y <= height
+                coordinate_map[meta.x, meta.y] = idx
+            end
+        end
+        println("DEBUG: Coordinate map built.")
+
+        close(stream)
+
+        source = ImzMLSource(hIbd, default_mz_format, default_intensity_format)
+        println("DEBUG: Creating MSIData object.")
+        return MSIData(source, spectra_metadata, (width, height), coordinate_map, cache_size)
+
+    catch e
+        close(stream)
+        close(hIbd)
+        rethrow(e)
+    end
+end
+
+function parse_uncompressed(stream, hIbd, param_groups, width, height, num_spectra,
+                              mz_format, intensity_format, mz_is_compressed, int_is_compressed, global_mode)
+    # Your existing working skip-based parser
     println("DEBUG: Learning file structure from first spectrum...")
     start_of_spectra_xml = position(stream)
     attr = get_spectrum_attributes(stream, hIbd)
@@ -188,9 +315,11 @@ function load_imzml_lazy(file_path::String; cache_size=100)
     spectra_metadata = Vector{SpectrumMetadata}(undef, num_spectra)
     mz_is_first = attr[3] == 3
 
-        println("DEBUG: Parsing metadata for $num_spectra spectra using skip-based method...")
     for k in 1:num_spectra
-            # Use skip values learned from the first spectrum, assuming all are identical.
+        # Store the start position of this spectrum for mode detection
+        spectrum_start_pos = position(stream)
+        
+        # Use skip values learned from the first spectrum
         skip(stream, attr[5]) # Skip to X coordinate value
         val_tag_x = find_tag(stream, r"value=\"(\d+)\"")
         x = parse(Int32, val_tag_x.captures[1])
@@ -203,6 +332,7 @@ function load_imzml_lazy(file_path::String; cache_size=100)
         val_tag_len = find_tag(stream, r"value=\"(\d+)\"")
         nPoints = parse(Int32, val_tag_len.captures[1])
 
+        # For uncompressed data, use simple calculation
         mz_len_bytes = nPoints * sizeof(mz_format)
         int_len_bytes = nPoints * sizeof(intensity_format)
 
@@ -215,49 +345,299 @@ function load_imzml_lazy(file_path::String; cache_size=100)
             mz_offset = int_offset + int_len_bytes
         end
 
-            # Create modern SpectrumAsset objects
+        # Mode detection from spectrum XML
+        current_pos = position(stream)
+        seek(stream, spectrum_start_pos)
+        spectrum_buffer = IOBuffer()
+        line = ""
+        while !eof(stream)
+            line = readline(stream)
+            write(spectrum_buffer, line)
+            if occursin("</spectrum>", line)
+                break
+            end
+        end
+        spectrum_xml = String(take!(spectrum_buffer))
+        
+        spectrum_mode = global_mode
+        if occursin("MS:1000127", spectrum_xml) 
+            spectrum_mode = CENTROID
+        elseif occursin("MS:1000128", spectrum_xml)
+            spectrum_mode = PROFILE
+        end
+        seek(stream, current_pos)
+
+        # Create SpectrumAsset objects
         mz_asset = SpectrumAsset(mz_format, mz_is_compressed, mz_offset, nPoints, :mz)
         int_asset = SpectrumAsset(intensity_format, int_is_compressed, int_offset, nPoints, :intensity)
         
-            spectra_metadata[k] = SpectrumMetadata(x, y, "", mz_asset, int_asset)
+        spectra_metadata[k] = SpectrumMetadata(x, y, "", spectrum_mode, mz_asset, int_asset)
         
-            # Advance the offset for the next spectrum's data.
         current_ibd_offset += mz_len_bytes + int_len_bytes
-            
         skip(stream, attr[8]) # Skip to the end of the spectrum tag
     end
-        # --- END OF NEW PARSING LOGIC ---
 
-        println("DEBUG: Metadata parsing complete.")
+    return spectra_metadata
+end
 
-        # Build coordinate map for imzML files
+function parse_compressed(stream, hIbd, param_groups, width, height, num_spectra,
-        println("DEBUG: Building coordinate map...")
+                              default_mz_format, default_intensity_format, 
-        coordinate_map = zeros(Int, width, height)
+                              mz_is_compressed, int_is_compressed, global_mode)
-        for (idx, meta) in enumerate(spectra_metadata)
+    # New parser for compressed data
-            if 1 <= meta.x <= width && 1 <= meta.y <= height
+    spectra_metadata = Vector{SpectrumMetadata}(undef, num_spectra)
-                coordinate_map[meta.x, meta.y] = idx
+
+    for k in 1:num_spectra
+        # Read the full spectrum XML block
+        spectrum_buffer = IOBuffer()
+        line = ""
+        while !eof(stream)
+            line = readline(stream)
+            if occursin("<spectrum ", line)
+                write(spectrum_buffer, line)
+                break
             end
         end
-        println("DEBUG: Coordinate map built.")
+        while !eof(stream)
-
+            line = readline(stream)
-        close(stream)
+            write(spectrum_buffer, line)
-
+            if occursin("</spectrum>", line)
-        source = ImzMLSource(hIbd, mz_format, intensity_format)
+                break
-        println("DEBUG: Creating MSIData object.")
-        return MSIData(source, spectra_metadata, (width, height), coordinate_map, cache_size)
-
-    catch e
-        close(stream)
-        close(hIbd)
-        rethrow(e)
             end
         end
+        spectrum_xml = String(take!(spectrum_buffer))
+
+        # Parse coordinates
+        x_match = match(r"IMS:1000050.*?value=\"(\d+)\"", spectrum_xml)
+        y_match = match(r"IMS:1000051.*?value=\"(\d+)\"", spectrum_xml)
+        x = x_match !== nothing ? parse(Int32, x_match.captures[1]) : Int32(0)
+        y = y_match !== nothing ? parse(Int32, y_match.captures[1]) : Int32(0)
+
+        # Parse mode
+        spectrum_mode = global_mode
+        if occursin("MS:1000127", spectrum_xml) 
+            spectrum_mode = CENTROID
+        elseif occursin("MS:1000128", spectrum_xml)
+            spectrum_mode = PROFILE
+        end
+
+        # Parse binary data arrays
+        array_data = []
+        
+        # Find all binaryDataArray blocks
+        array_matches = eachmatch(r"<binaryDataArray.*?<\/binaryDataArray>"s, spectrum_xml)
+        for array_match in array_matches
+            array_xml = array_match.match
+            
+            # Determine if this is m/z or intensity array
+            is_mz = occursin("MS:1000514", array_xml) || occursin("mzArray", array_xml)
+            
+            # Parse external data parameters
+            # Get array_length (nPoints)
+            array_len_cv_match = match(r"IMS:1000103.*?value=\"(\d+)\"", array_xml)
+            array_length = 0
+            if array_len_cv_match !== nothing
+                array_length = parse(Int32, array_len_cv_match.captures[1])
+            end
+            if array_length == 0
+                nPoints_match = match(r"defaultArrayLength=\"(\d+)\"", spectrum_xml)
+                if nPoints_match !== nothing
+                    array_length = parse(Int32, nPoints_match.captures[1])
+                end
+            end
+
+            # Get encoded_length
+            encoded_len_cv_match = match(r"IMS:1000104.*?value=\"(\d+)\"", array_xml)
+            encoded_length = 0
+            if encoded_len_cv_match !== nothing
+                encoded_length = parse(Int64, encoded_len_cv_match.captures[1])
+            else
+                encoded_len_attr_match = match(r"encodedLength=\"(\d+)\"", array_xml)
+                if encoded_len_attr_match !== nothing
+                    encoded_length = parse(Int64, encoded_len_attr_match.captures[1])
+                end
+            end
+
+            # Get offset
+            offset_match = match(r"IMS:1000102.*?value=\"(\d+)\"", array_xml)
+            offset = 0
+            if offset_match !== nothing
+                offset = parse(Int64, offset_match.captures[1])
+            end
+            
+            if array_length > 0 && offset > 0
+                push!(array_data, (
+                    is_mz = is_mz,
+                    array_length = array_length,
+                    encoded_length = encoded_length,
+                    offset = offset
+                ))
+            end
+        end
+
+        # Separate m/z and intensity arrays
+        mz_data = filter(d -> d.is_mz, array_data)
+        int_data = filter(d -> !d.is_mz, array_data)
+        
+        if length(mz_data) != 1 || length(int_data) != 1
+            error("Spectrum $k: Expected exactly one m/z and one intensity array")
+        end
+
+        mz_info = mz_data[1]
+        int_info = int_data[1]
+
+        # DEBUG: Print first spectrum details
+        if k == 1
+            println("DEBUG First spectrum parsed:")
+            println("  Coordinates: x=$x, y=$y")
+            println("  Mode: $spectrum_mode")
+            println("  m/z array: array_length=$(mz_info.array_length), encoded_length=$(mz_info.encoded_length), offset=$(mz_info.offset)")
+            println("  intensity array: array_length=$(int_info.array_length), encoded_length=$(int_info.encoded_length), offset=$(int_info.offset)")
+            println("  Expected m/z bytes: $(mz_info.array_length * sizeof(default_mz_format))")
+            println("  Expected intensity bytes: $(int_info.array_length * sizeof(default_intensity_format))")
+        end
+
+        # Create SpectrumAsset objects
+        mz_asset = SpectrumAsset(default_mz_format, mz_is_compressed, mz_info.offset, 
+                                mz_is_compressed ? mz_info.encoded_length : mz_info.array_length, :mz)
+        int_asset = SpectrumAsset(default_intensity_format, int_is_compressed, int_info.offset,
+                                 int_is_compressed ? int_info.encoded_length : int_info.array_length, :intensity)
+        
+        spectra_metadata[k] = SpectrumMetadata(x, y, "", spectrum_mode, mz_asset, int_asset)
+    end
+
+    return spectra_metadata
+end
+
+function parse_neofx(stream, hIbd, param_groups, width, height, num_spectra,
+                              default_mz_format, default_intensity_format, 
+                              mz_is_compressed, int_is_compressed, global_mode)
+    # New parser for compressed data
+    spectra_metadata = Vector{SpectrumMetadata}(undef, num_spectra)
+
+    for k in 1:num_spectra
+        # Read the full spectrum XML block
+        spectrum_buffer = IOBuffer()
+        line = ""
+        while !eof(stream)
+            line = readline(stream)
+            if occursin("<spectrum ", line)
+                write(spectrum_buffer, line)
+                break
+            end
+        end
+        while !eof(stream)
+            line = readline(stream)
+            write(spectrum_buffer, line)
+            if occursin("</spectrum>", line)
+                break
+            end
+        end
+        spectrum_xml = String(take!(spectrum_buffer))
+
+        # Parse coordinates
+        x_match = match(r"IMS:1000050.*?value=\"(\d+)\"", spectrum_xml)
+        y_match = match(r"IMS:1000051.*?value=\"(\d+)\"", spectrum_xml)
+        x = x_match !== nothing ? parse(Int32, x_match.captures[1]) : Int32(0)
+        y = y_match !== nothing ? parse(Int32, y_match.captures[1]) : Int32(0)
+
+        # Parse mode
+        spectrum_mode = global_mode
+        if occursin("MS:1000127", spectrum_xml) 
+            spectrum_mode = CENTROID
+        elseif occursin("MS:1000128", spectrum_xml)
+            spectrum_mode = PROFILE
+        end
+
+        # Parse binary data arrays
+        array_data = []
+        
+        # Find all binaryDataArray blocks
+        array_matches = eachmatch(r"<binaryDataArray.*?<\/binaryDataArray>"s, spectrum_xml)
+        for array_match in array_matches
+            array_xml = array_match.match
+            
+            # Determine if this is m/z or intensity array
+            is_mz = occursin("MS:1000514", array_xml) || occursin("mzArray", array_xml)
+            
+            # Parse external data parameters
+            # Get array_length (nPoints)
+            array_len_cv_match = match(r"IMS:1000103.*?value=\"(\d+)\"", array_xml)
+            array_length = 0
+            if array_len_cv_match !== nothing
+                array_length = parse(Int32, array_len_cv_match.captures[1])
+            end
+            if array_length == 0
+                nPoints_match = match(r"defaultArrayLength=\"(\d+)\"", spectrum_xml)
+                if nPoints_match !== nothing
+                    array_length = parse(Int32, nPoints_match.captures[1])
+                end
+            end
+
+            # Get encoded_length
+            encoded_len_cv_match = match(r"IMS:1000104.*?value=\"(\d+)\"", array_xml)
+            encoded_length = 0
+            if encoded_len_cv_match !== nothing
+                encoded_length = parse(Int64, encoded_len_cv_match.captures[1])
+            else
+                encoded_len_attr_match = match(r"encodedLength=\"(\d+)\"", array_xml)
+                if encoded_len_attr_match !== nothing
+                    encoded_length = parse(Int64, encoded_len_attr_match.captures[1])
+                end
+            end
+
+            # Get offset
+            offset_match = match(r"IMS:1000102.*?value=\"(\d+)\"", array_xml)
+            offset = 0
+            if offset_match !== nothing
+                offset = parse(Int64, offset_match.captures[1])
+            end
+            
+            if array_length > 0 && offset > 0
+                push!(array_data, (
+                    is_mz = is_mz,
+                    array_length = array_length,
+                    encoded_length = encoded_length,
+                    offset = offset
+                ))
+            end
+        end
+
+        # Separate m/z and intensity arrays
+        mz_data = filter(d -> d.is_mz, array_data)
+        int_data = filter(d -> !d.is_mz, array_data)
+        
+        if length(mz_data) != 1 || length(int_data) != 1
+            error("Spectrum $k: Expected exactly one m/z and one intensity array")
+        end
+
+        mz_info = mz_data[1]
+        int_info = int_data[1]
+
+        # DEBUG: Print first spectrum details
+        if k == 1
+            println("DEBUG First spectrum parsed:")
+            println("  Coordinates: x=$x, y=$y")
+            println("  Mode: $spectrum_mode")
+            println("  m/z array: array_length=$(mz_info.array_length), encoded_length=$(mz_info.encoded_length), offset=$(mz_info.offset)")
+            println("  intensity array: array_length=$(int_info.array_length), encoded_length=$(int_info.encoded_length), offset=$(int_info.offset)")
+            println("  Expected m/z bytes: $(mz_info.array_length * sizeof(default_mz_format))")
+            println("  Expected intensity bytes: $(int_info.array_length * sizeof(default_intensity_format))")
+        end
+
+        # Create SpectrumAsset objects
+        mz_asset = SpectrumAsset(default_mz_format, mz_is_compressed, mz_info.offset, 
+                                mz_is_compressed ? mz_info.encoded_length : mz_info.array_length, :mz)
+        int_asset = SpectrumAsset(default_intensity_format, int_is_compressed, int_info.offset,
+                                 int_is_compressed ? int_info.encoded_length : int_info.array_length, :intensity)
+        
+        spectra_metadata[k] = SpectrumMetadata(x, y, "", spectrum_mode, mz_asset, int_asset)
+    end
+
+    return spectra_metadata
+end
 
 # --- End of content from imzML.jl ---
 
-
-# --- Start of content from Imaging_Normalization.jl ---
-
 # =============================================================================
 #
 # Image Slice Extraction
@@ -446,7 +826,8 @@ function plot_slice(msi_data::MSIData, mass::Real, tolerance::Real, output_dir::
     fig = Figure(size = (600, 500))
     ax = CairoMakie.Axis(fig[1, 1],
         aspect=DataAspect(),
-        title=@sprintf("Slice for m/z: %.2f", mass)
+        title=@sprintf("Slice for m/z: %.2f", mass),
+        yreversed=true
     )
     hidedecorations!(ax)
 

test/run_tests.jl

@@ -52,15 +52,19 @@ const CONVERSION_TARGET_IMZML = "test/results/converted_mzml.imzML"
 
 # --- Test Case 3: Standard .imzML file ---
 # An existing imzML file (can be the one generated from Case 2).
-const TEST_IMZML_FILE = CONVERSION_TARGET_IMZML # The output from case 2
+# const TEST_IMZML_FILE = CONVERSION_TARGET_IMZML # The output from case 2
 # const TEST_IMZML_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/imzML_AP_SMALDI/HR2MSImouseurinarybladderS096.imzML"
-# const TEST_IMZML_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/Imaging_paper_spray/Imaging_paper_spray.imzML"
+# const TEST_IMZML_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/Imaging_paper_spray/Imaging_paper_spray.imzML" #profile
 # const TEST_IMZML_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/Imaging prueba Roya 1/royaimg.imzML"
+# const TEST_IMZML_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/salida/ltpmsi-chilli.imzML" # centroid aparently?
+# const TEST_IMZML_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/salida/Stomach_DHB_compressed.imzML" # centroid compressed
+const TEST_IMZML_FILE = "/home/pixel/Documents/Cinvestav_2025/Analisis/salida/Stomach_DHB_uncompressed.imzML" # centroid
 # The m/z value to use for creating an image slice.
 # const MZ_VALUE_FOR_SLICE = 309.06 # BF
 # const MZ_VALUE_FOR_SLICE = 896.0 # HR2MSI
 # const MZ_VALUE_FOR_SLICE = 76.03 # I PS
-const MZ_VALUE_FOR_SLICE = 313 # ROYA
+# const MZ_VALUE_FOR_SLICE = 313 # ROYA
+const MZ_VALUE_FOR_SLICE = 100 # advanced processing
 # const MZ_TOLERANCE = 0.1
 # const MZ_TOLERANCE = 1
 const MZ_TOLERANCE = 0.1
@@ -71,8 +75,8 @@ const COORDS_TO_PLOT = (50, 50) # Example coordinates (X, Y)
 # --- Output Directory ---
 const RESULTS_DIR = "test/results"
 
-test1 = true
+test1 = false
-test2 = true 
+test2 = false 
 test3 = true
 
 # ===================================================================
@@ -135,6 +139,30 @@ function validate_msi_data(filepath::String)
     end
 end
 
+function debug_xml_parsing(file_path::String)
+    println("=== DEBUG XML PARSING ===")
+    stream = open(file_path, "r")
+    
+    # Find and print the first spectrum
+    while !eof(stream)
+        line = readline(stream)
+        if occursin("<spectrum", line)
+            println("FOUND FIRST SPECTRUM:")
+            spectrum_xml = line
+            # Read until end of spectrum
+            while !eof(stream) && !occursin("</spectrum>", line)
+                line = readline(stream)
+                spectrum_xml *= line
+            end
+            println("SPECTRUM XML:")
+            println(spectrum_xml)
+            break
+        end
+    end
+    close(stream)
+    println("=== END DEBUG ===")
+end
+
 
 # ===================================================================
 # TEST RUNNER
@@ -229,16 +257,24 @@ function run_test()
 
         # Also run tests for plotting spectrum and image slice
         if isfile(TEST_IMZML_FILE)
+            debug_xml_parsing(TEST_IMZML_FILE)
+            msi_data = @time OpenMSIData(TEST_IMZML_FILE)
+            precompute_analytics(msi_data)
             # Add spectrum plotting for imzML to match Test Case 1
             try
+                
                 # Get the msi data from the imzml
                 println("Plotting a sample spectrum from $TEST_IMZML_FILE...")
-                msi_data = @time OpenMSIData(TEST_IMZML_FILE)
+                
-                x_coord, y_coord = COORDS_TO_PLOT
+                # Use coordinates from the first spectrum in the metadata
+                first_spectrum_meta = msi_data.spectra_metadata[1]
+                x_coord = first_spectrum_meta.x
+                y_coord = first_spectrum_meta.y
+                
+                println("DIAGNOSTIC_READ: Reading from coordinate_map[$x_coord, $y_coord]. Value is $(msi_data.coordinate_map[x_coord, y_coord]).")
                 
                 # Get the x y coordinate spectrum data
-                mz, intensity = GetSpectrum(msi_data, x_coord, y_coord)
+                mz, intensity = GetSpectrum(msi_data, Int(x_coord), Int(y_coord))
-                
                 # Plot the data
                 fig = Figure(size = (800, 600))
                 ax = Axis(fig[1, 1], xlabel="m/z", ylabel="Intensity", title="Spectrum at ($x_coord, $y_coord) from $(basename(TEST_IMZML_FILE))")
@@ -276,7 +312,7 @@ function run_test()
                 output_path = joinpath(RESULTS_DIR, "test_imzml_average_spectrum.png")
                 save(output_path, fig)
                 println("SUCCESS: Total spectrum plot saved to $output_path")
-                println("No spectrums tested on this try.")
+                # println("No spectrums tested on this try.")
             catch e
                 println("ERROR during spectrum plotting in Test Case 3: $e")
             end
@@ -284,8 +320,13 @@ function run_test()
             # Test the plot_slice function
             try
                 println("Testing plot_slice function on $TEST_IMZML_FILE...")
-                msi_data = @time OpenMSIData(TEST_IMZML_FILE)
+                
-                @time plot_slice(msi_data, MZ_VALUE_FOR_SLICE, MZ_TOLERANCE, RESULTS_DIR, stage_name="test_imzml_single_slice")
+                # Use the base peak m/z from the first spectrum for the slice
+                # Or a more general approach: use the global max intensity m/z
+                # For now, let's use the base peak m/z of the first spectrum
+                slice_mz_value = msi_data.spectrum_stats_df.BasePeakMZ[1]
+                
+                @time plot_slice(msi_data, slice_mz_value, MZ_TOLERANCE, RESULTS_DIR, stage_name="test_imzml_single_slice")
                 # The success message is now inside plot_slice
             catch e
                 println("ERROR during plot_slice test in Test Case 3: $e")