Merge branch 'add_dual_color_bruker' of CatalystNeuro/ophys_testing_data into main

Very nice!

imaging_datasets/BrukerTif/NCCR62_2023_07_06_IntoTheVoid_t_series_Dual_color-000/NCCR62_2023_07_06_IntoTheVoid_t_series_Dual_color-000.xml

@@ -0,0 +1,176 @@
+<?xml version="1.0" encoding="utf-8"?>
+<PVScan version="5.8.64.200" date="7/6/2023 3:13:58 PM" notes="">
+  <SystemIDs SystemID="E8D0-2F5E-B967-36D1-3CA0-8C25-681B-CEF3">
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+  </SystemIDs>
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+    <PVStateValue key="bitDepth" value="13" />
+    <PVStateValue key="currentScanAmplitude">
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+      <IndexedValue index="YAxis" value="4.17170481" />
+    </PVStateValue>
+    <PVStateValue key="currentScanCenter">
+      <IndexedValue index="XAxis" value="0" />
+      <IndexedValue index="YAxis" value="0" />
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+    <PVStateValue key="daqGain">
+      <IndexedValue index="0" value="1" description="±1.25V" />
+      <IndexedValue index="1" value="-1" description="±1.25V" />
+      <IndexedValue index="2" value="-1" description="±1.25V" />
+    </PVStateValue>
+    <PVStateValue key="dwellTime" value="0.4" />
+    <PVStateValue key="framePeriod" value="0.032963778" />
+    <PVStateValue key="interlacedScanTrackCount" value="0" />
+    <PVStateValue key="laserPower">
+      <IndexedValue index="0" value="450.1953125" description="920 Axon" />
+      <IndexedValue index="1" value="500" description="1064 Axon" />
+      <IndexedValue index="2" value="2.21946022727273" description="Monaco" />
+    </PVStateValue>
+    <PVStateValue key="linesPerFrame" value="512" />
+    <PVStateValue key="maxVoltage">
+      <IndexedValue index="XAxis" value="2.085852405" />
+      <IndexedValue index="YAxis" value="2.085852405" />
+    </PVStateValue>
+    <PVStateValue key="micronsPerPixel">
+      <IndexedValue index="XAxis" value="1.1078125" />
+      <IndexedValue index="YAxis" value="1.1078125" />
+      <IndexedValue index="ZAxis" value="5" />
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+    <PVStateValue key="minVoltage">
+      <IndexedValue index="XAxis" value="-2.085852405" />
+      <IndexedValue index="YAxis" value="-2.085852405" />
+    </PVStateValue>
+    <PVStateValue key="objectiveLens" value="16X" />
+    <PVStateValue key="objectiveLensMag" value="16" />
+    <PVStateValue key="objectiveLensNA" value="0.8" />
+    <PVStateValue key="opticalZoom" value="2" />
+    <PVStateValue key="pixelsPerLine" value="512" />
+    <PVStateValue key="pmtGain">
+      <IndexedValue index="0" value="750" description="PMT 1 HV (Red)" />
+      <IndexedValue index="1" value="750" description="PMT 2 HV (Green)" />
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+    <PVStateValue key="positionCurrent">
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+      <SubindexedValues index="YAxis">
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+      <SubindexedValues index="ZAxis">
+        <SubindexedValue subindex="0" value="130.025" description="Z Focus" />
+        <SubindexedValue subindex="1" value="0" description="Narrow NeuraLeap" />
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+    </PVStateValue>
+    <PVStateValue key="preampFilter" value="NoFilter" description="None" />
+    <PVStateValue key="preampOffset">
+      <SubindexedValues index="0">
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+        <SubindexedValue subindex="1" value="0.01" description="Ch2" />
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+    <PVStateValue key="rastersPerFrame" value="1" />
+    <PVStateValue key="rotation" value="0" />
+    <PVStateValue key="samplesPerPixel" value="3" />
+    <PVStateValue key="scanLinePeriod" value="6.3149E-05" />
+    <PVStateValue key="useInterlacedScanPattern" value="False" />
+    <PVStateValue key="xYStageGridIndex" value="-1" />
+    <PVStateValue key="xYStageGridXIndex" value="-1" />
+    <PVStateValue key="xYStageGridYIndex" value="-1" />
+    <PVStateValue key="yAspectExpansion" value="1" />
+    <PVStateValue key="zDevice" value="0" />
+  </PVStateShard>
+  <Sequence type="TSeries Timed Element" cycle="1" time="15:13:59.3902751" xYStageGridDefined="False" xYStageGridNumXPositions="0" xYStageGridNumYPositions="0" xYStageGridOverlapPercentage="10" xYStageGridXOverlap="10" xYStageGridYOverlap="10">
+    <PVStateShard />
+    <Frame relativeTime="0" absoluteTime="2.14300000000003" index="1" parameterSet="CurrentSettings">
+      <File channel="1" channelName="Ch1" page="1" filename="NCCR62_2023_07_06_IntoTheVoid_t_series_Dual_color-000_Cycle00001_Ch1_000001.ome.tif" />
+      <File channel="2" channelName="Ch2" page="1" filename="NCCR62_2023_07_06_IntoTheVoid_t_series_Dual_color-000_Cycle00001_Ch2_000001.ome.tif" />
+      <ExtraParameters lastGoodFrame="0" />
+      <PVStateShard>
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+        <PVStateValue key="scanLinePeriod" value="6.314E-05" />
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+    </Frame>
+    <Frame relativeTime="0.033474355" absoluteTime="2.17647435500003" index="2" parameterSet="CurrentSettings">
+      <File channel="1" channelName="Ch1" page="2" filename="NCCR62_2023_07_06_IntoTheVoid_t_series_Dual_color-000_Cycle00001_Ch1_000001.ome.tif" />
+      <File channel="2" channelName="Ch2" page="2" filename="NCCR62_2023_07_06_IntoTheVoid_t_series_Dual_color-000_Cycle00001_Ch2_000001.ome.tif" />
+      <ExtraParameters lastGoodFrame="0" />
+      <PVStateShard>
+        <PVStateValue key="framePeriod" value="0.033474355" />
+        <PVStateValue key="scanLinePeriod" value="6.314E-05" />
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+    </Frame>
+    <Frame relativeTime="0.06694871" absoluteTime="2.20994871000003" index="3" parameterSet="CurrentSettings">
+      <File channel="1" channelName="Ch1" page="3" filename="NCCR62_2023_07_06_IntoTheVoid_t_series_Dual_color-000_Cycle00001_Ch1_000001.ome.tif" />
+      <File channel="2" channelName="Ch2" page="3" filename="NCCR62_2023_07_06_IntoTheVoid_t_series_Dual_color-000_Cycle00001_Ch2_000001.ome.tif" />
+      <ExtraParameters lastGoodFrame="0" />
+      <PVStateShard>
+        <PVStateValue key="framePeriod" value="0.033474355" />
+        <PVStateValue key="scanLinePeriod" value="6.314E-05" />
+      </PVStateShard>
+    </Frame>
+    <Frame relativeTime="0.100423065" absoluteTime="2.24342306500003" index="4" parameterSet="CurrentSettings">
+      <File channel="1" channelName="Ch1" page="4" filename="NCCR62_2023_07_06_IntoTheVoid_t_series_Dual_color-000_Cycle00001_Ch1_000001.ome.tif" />
+      <File channel="2" channelName="Ch2" page="4" filename="NCCR62_2023_07_06_IntoTheVoid_t_series_Dual_color-000_Cycle00001_Ch2_000001.ome.tif" />
+      <ExtraParameters lastGoodFrame="0" />
+      <PVStateShard>
+        <PVStateValue key="framePeriod" value="0.033474355" />
+        <PVStateValue key="scanLinePeriod" value="6.314E-05" />
+      </PVStateShard>
+    </Frame>
+    <Frame relativeTime="0.13389742" absoluteTime="2.27689742000003" index="5" parameterSet="CurrentSettings">
+      <File channel="1" channelName="Ch1" page="5" filename="NCCR62_2023_07_06_IntoTheVoid_t_series_Dual_color-000_Cycle00001_Ch1_000001.ome.tif" />
+      <File channel="2" channelName="Ch2" page="5" filename="NCCR62_2023_07_06_IntoTheVoid_t_series_Dual_color-000_Cycle00001_Ch2_000001.ome.tif" />
+      <ExtraParameters lastGoodFrame="0" />
+      <PVStateShard>
+        <PVStateValue key="framePeriod" value="0.033474355" />
+        <PVStateValue key="scanLinePeriod" value="6.314E-05" />
+      </PVStateShard>
+    </Frame>
+    <Frame relativeTime="0.167371775" absoluteTime="2.31037177500003" index="6" parameterSet="CurrentSettings">
+      <File channel="1" channelName="Ch1" page="6" filename="NCCR62_2023_07_06_IntoTheVoid_t_series_Dual_color-000_Cycle00001_Ch1_000001.ome.tif" />
+      <File channel="2" channelName="Ch2" page="6" filename="NCCR62_2023_07_06_IntoTheVoid_t_series_Dual_color-000_Cycle00001_Ch2_000001.ome.tif" />
+      <ExtraParameters lastGoodFrame="0" />
+      <PVStateShard>
+        <PVStateValue key="framePeriod" value="0.033474355" />
+        <PVStateValue key="scanLinePeriod" value="6.314E-05" />
+      </PVStateShard>
+    </Frame>
+    <Frame relativeTime="0.20084613" absoluteTime="2.34384613000003" index="7" parameterSet="CurrentSettings">
+      <File channel="1" channelName="Ch1" page="7" filename="NCCR62_2023_07_06_IntoTheVoid_t_series_Dual_color-000_Cycle00001_Ch1_000001.ome.tif" />
+      <File channel="2" channelName="Ch2" page="7" filename="NCCR62_2023_07_06_IntoTheVoid_t_series_Dual_color-000_Cycle00001_Ch2_000001.ome.tif" />
+      <ExtraParameters lastGoodFrame="0" />
+      <PVStateShard>
+        <PVStateValue key="framePeriod" value="0.033474355" />
+        <PVStateValue key="scanLinePeriod" value="6.314E-05" />
+      </PVStateShard>
+    </Frame>
+    <Frame relativeTime="0.234320485" absoluteTime="2.37732048500003" index="8" parameterSet="CurrentSettings">
+      <File channel="1" channelName="Ch1" page="8" filename="NCCR62_2023_07_06_IntoTheVoid_t_series_Dual_color-000_Cycle00001_Ch1_000001.ome.tif" />
+      <File channel="2" channelName="Ch2" page="8" filename="NCCR62_2023_07_06_IntoTheVoid_t_series_Dual_color-000_Cycle00001_Ch2_000001.ome.tif" />
+      <ExtraParameters lastGoodFrame="0" />
+      <PVStateShard>
+        <PVStateValue key="framePeriod" value="0.033474355" />
+        <PVStateValue key="scanLinePeriod" value="6.314E-05" />
+      </PVStateShard>
+    </Frame>
+    <Frame relativeTime="0.26779484" absoluteTime="2.41079484000003" index="9" parameterSet="CurrentSettings">
+      <File channel="1" channelName="Ch1" page="9" filename="NCCR62_2023_07_06_IntoTheVoid_t_series_Dual_color-000_Cycle00001_Ch1_000001.ome.tif" />
+      <File channel="2" channelName="Ch2" page="9" filename="NCCR62_2023_07_06_IntoTheVoid_t_series_Dual_color-000_Cycle00001_Ch2_000001.ome.tif" />
+      <ExtraParameters lastGoodFrame="0" />
+      <PVStateShard>
+        <PVStateValue key="framePeriod" value="0.033474355" />
+        <PVStateValue key="scanLinePeriod" value="6.314E-05" />
+      </PVStateShard>
+    </Frame>
+    <Frame relativeTime="0.301269195" absoluteTime="2.44426919500003" index="10" parameterSet="CurrentSettings">
+      <File channel="1" channelName="Ch1" page="10" filename="NCCR62_2023_07_06_IntoTheVoid_t_series_Dual_color-000_Cycle00001_Ch1_000001.ome.tif" />
+      <File channel="2" channelName="Ch2" page="10" filename="NCCR62_2023_07_06_IntoTheVoid_t_series_Dual_color-000_Cycle00001_Ch2_000001.ome.tif" />
+      <ExtraParameters lastGoodFrame="0" />
+      <PVStateShard>
+        <PVStateValue key="framePeriod" value="0.033474355" />
+        <PVStateValue key="scanLinePeriod" value="6.314E-05" />
+      </PVStateShard>
+    </Frame>
+  </Sequence>
+</PVScan>

imaging_datasets/BrukerTif/README.md

@@ -1,14 +1,19 @@
 # Bruker TIF format
 
 This format consists of multiple OME-TIF image files (.ome.tif files) and configuration parameters in XML format (.xml and/or .env files).
-Each OME-TIF file contains a single a frame, the order and timing of frames and other metadata can be retrieved from the XML file.
+Each OME-TIF file can contain a single frame (single page tiffs), or they can contain stacks of images (multi-page tiffs). 
+Each folder contains an XML file with the order and timing of images, the number of optical channels, the number of imaging planes and other useful information.
 
 The following examples were shared with us by the Pinto lab.
 
 ## NCCR32_2023_02_20_Into_the_void_t_series_baseline-000
 
-This folder contains the first 10 tiffs from a 2P recording with a single imaging plane (and one color channel). The XML file contains the order and timing of images and other useful metadata.
+This folder contains an XML file and the first 10 `.ome.tif` files from a 2P recording with a single imaging plane (and one color channel). 
 
 ## NCCR32_2022_11_03_IntoTheVoid_t_series-005
 
-This folder contains first 10 tiffs (5 frames from two imaging planes) from a volumetric 2P recording. The XML file contains the order and timing of images, the number of imaging planes and other useful metadata.
+This folder contains an XML file and the first 10 `.ome.tif` files (5 frames from two imaging planes) from a volumetric 2P recording. 
+
+## NCCR62_2023_07_06_IntoTheVoid_t_series_Dual_color-000
+
+This folder contains an XML file and 2 `.ome.tif` files (10-10 frames for each optical channel) from a 2P recording with a single imaging plane and two channels.