[ome-users] bio-formats Micromanager reader issue
Colin Fuller
cjfuller at gmail.com
Fri Jun 1 23:37:54 BST 2012
Hi--
When attempting to read a micromanager file using the bio-formats ImageJ
plugin (v. 4.3.3 as well as the latest trunk build, running latest Fiji on
ubuntu 12.04), I've encountered an exception with the stack trace included
below. I think this results from micromanager having created a metadata
field with a value of only empty square brackets in the metadata.txt file.
I've attached a sample metadata.txt file (one of the empty fields is
"CustomIntervals_ms": [] at line 47, e.g.); I'm happy to ftp the actual
images to you as well, though they are too large to attach.
Thanks,
Colin Fuller
Stack trace:
java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at ij.Command.runPlugIn(Command.java:146)
at ij.Command.runCommand(Command.java:95)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.StringIndexOutOfBoundsException: String index out of
range: -1
at java.lang.String.substring(String.java:1937)
at loci.formats.in.MicromanagerReader.initFile(MicromanagerReader.java:285)
at loci.formats.FormatReader.setId(FormatReader.java:1072)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:481)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
at loci.plugins.in.Importer.showDialogs(Importer.java:125)
at loci.plugins.in.Importer.run(Importer.java:77)
at loci.plugins.LociImporter.run(LociImporter.java:79)
at ij.IJ.runUserPlugIn(IJ.java:185)
at ij.IJ.runPlugIn(IJ.java:152)
... 8 more
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{
"Summary": {
"Slices": 9,
"Interval_ms": 0,
"UUID": "775aaa0b-87c9-4142-9586-d508da358802",
"UserName": "cfuller",
"Depth": 2,
"PixelType": "GRAY16",
"Time": "2012-06-01 10:14:40 -0700",
"Date": "2012-06-01",
"z-step_um": 0.25,
"MetadataVersion": 10,
"PositionIndex": 0,
"SlicesFirst": false,
"ChContrastMin": [
2147483647,
2147483647,
2147483647
],
"Width": 1392,
"PixelAspect": 1,
"MicroManagerVersion": "1.4.10",
"ROI": [
0,
0,
1392,
1040
],
"ChNames": [
"DAPI",
"FITC",
"RHOD"
],
"IJType": 1,
"GridRow": 0,
"Comment": "",
"Height": 1040,
"GridColumn": 0,
"Prefix": "20120601_fiberspreads_flowcell_T",
"PixelSize_um": 0,
"Frames": 0,
"BitDepth": 12,
"KeepShutterOpenChannels": true,
"Source": "Micro-Manager",
"Channels": 3,
"ComputerName": "horntail",
"CustomIntervals_ms": [],
"KeepShutterOpenSlices": false,
"ChColors": [
-16776961,
-16711936,
-65536
],
"TimeFirst": false,
"ChContrastMax": [
-2147483648,
-2147483648,
-2147483648
],
"Positions": 0,
"Directory": "C:\\Documents and Settings\\Colin Fuller/Images"
},
"FrameKey-0-0-0": {
"Core-Focus": "ZStage",
"Channel": "DAPI",
"Core-Initialize": "1",
"COM7-AnswerTimeout": "500.0000",
"CoolsnapHQ-ShutterMode": "Open Shutter Pre-Exposure",
"COM7-Handshaking": "Off",
"FrameIndex": 0,
"CoolsnapHQ-TransposeMirrorX": "0",
"CoolsnapHQ-TransposeMirrorY": "0",
"Wheel-B-State": "2",
"CoolsnapHQ-ClearMode": "Clear Pre-Exposure",
"CoolsnapHQ-TriggerMode": "Timed",
"Wheel-B-ClosedPosition": "",
"COM8-Name": "COM8",
"ZStage-Name": "ZStage",
"CoolsnapHQ-X-dimension": "1392",
"CoolsnapHQ-ChipName": "ICX285 ",
"CoolsnapHQ-PixelType": "12bit",
"CoolsnapHQ-PreampDelay": "1",
"CoolsnapHQ-PreampOffLimit": "10000",
"CoolsnapHQ-ReadoutRate": "10MHz 12bit",
"ZStage-Port": "COM8",
"Core-ImageProcessor": "",
"CoolsnapHQ-MaskLines": "11",
"CoolsnapHQ-TransposeCorrection": "0",
"CoolsnapHQ-Port": "Normal",
"SlicePosition": -1,
"Wheel-A-ClosedPosition": "",
"CoolsnapHQ-Gain": "2",
"Exposure-ms": 500,
"CoolsnapHQ-Description": "PVCAM API device adapter",
"ZStage-Axis": "Z",
"COM7-Description": "Serial port driver (boost:asio)",
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"Wheel-B-Label": "Filter-2",
"AxisPositions": null,
"COM8-Parity": "None",
"CoolsnapHQ-PMode": "Normal Parallel Clocking",
"Time": "2012-06-01 10:14:40 -0700",
"CoolsnapHQ-Binning": "1",
"Epi-Port": "COM7",
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"CoolsnapHQ-PVCAM Version": "2.7.6",
"Epi-Name": "Shutter-A 10-2",
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"BitDepth": 12,
"Slice": 0,
"CoolsnapHQ-CCDTemperatureSetPoint": "-30",
"Wheel-A-Label": "Filter-2",
"COM8-AnswerTimeout": "500.0000",
"Wheel-B-Description": "Sutter Lambda filter wheel adapter",
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"ChannelIndex": 0,
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"Core-Shutter": "Epi",
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"UUID": "d1a7d3e2-1853-47e9-a8b6-bf5de37b5c76",
"Epi-Description": "Sutter Lambda shutter adapter",
"Core-Camera": "CoolsnapHQ",
"CoolsnapHQ-PostscanPixels": "40",
"Core-TimeoutMs": "5000",
"Core-SLM": "",
"CoolsnapHQ-Trigger Timeout (secs)": "2",
"ZStage-Description": "ASI Z-stage driver adapter",
"ElapsedTime-ms": 1213,
"Wheel-A-Name": "Wheel-A",
"Wheel-B-Speed": "3",
"CoolsnapHQ-TransposeXY": "0",
"CoolsnapHQ-Firmware Version": "2132",
"Wheel-A-Description": "Sutter Lambda filter wheel adapter",
"Frame": 0,
"Wheel-A-Port": "COM7",
"Core-ChannelGroup": "Channel",
"PositionIndex": 0,
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"WaitInterval": 0,
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"Summary": {
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"UUID": "775aaa0b-87c9-4142-9586-d508da358802",
"UserName": "cfuller",
"Depth": 2,
"PixelType": "GRAY16",
"Time": "2012-06-01 10:14:40 -0700",
"Date": "2012-06-01",
"z-step_um": 0.25,
"MetadataVersion": 10,
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"SlicesFirst": false,
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2147483647,
2147483647,
2147483647
],
"Width": 1392,
"PixelAspect": 1,
"MicroManagerVersion": "1.4.10",
"ROI": [
0,
0,
1392,
1040
],
"ChNames": [
"DAPI",
"FITC",
"RHOD"
],
"IJType": 1,
"GridRow": 0,
"Comment": "",
"Height": 1040,
"GridColumn": 0,
"Prefix": "20120601_fiberspreads_flowcell_T",
"PixelSize_um": 0,
"Frames": 0,
"BitDepth": 12,
"KeepShutterOpenChannels": true,
"Source": "Micro-Manager",
"Channels": 3,
"ComputerName": "horntail",
"CustomIntervals_ms": [],
"KeepShutterOpenSlices": false,
"ChColors": [
-16776961,
-16711936,
-65536
],
"TimeFirst": false,
"ChContrastMax": [
-2147483648,
-2147483648,
-2147483648
],
"Positions": 0,
"Directory": "C:\\Documents and Settings\\Colin Fuller/Images"
},
"Source": "CoolsnapHQ",
"Wheel-A-Delay_ms": "0.0000",
"CoolsnapHQ-PrescanPixels": "21",
"CoolsnapHQ-CCDTemperature": "-30",
"COM8-DataBits": "8",
"Epi-Mode": "Fast",
"Binning": "1",
"CoolsnapHQ-OutputTriggerFirstMissing": "0",
"CoolsnapHQ-Y-dimension": "1040",
"Wheel-A-Speed": "3",
"Wheel-B-Delay_ms": "0.0000",
"Epi-State": "1",
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"CoolsnapHQ-FullWellCapacity": "16000",
"YPositionUm": null,
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"XPositionUm": null,
"CoolsnapHQ-Name": "CoolsnapHQ",
"FileName": "img_000000000_DAPI_000.tif",
"COM8-Description": "Serial port driver (boost:asio)",
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},
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"COM7-AnswerTimeout": "500.0000",
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"Wheel-B-State": "3",
"CoolsnapHQ-ClearMode": "Clear Pre-Exposure",
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"CoolsnapHQ-ChipName": "ICX285 ",
"CoolsnapHQ-PixelType": "12bit",
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"CoolsnapHQ-PreampOffLimit": "10000",
"CoolsnapHQ-ReadoutRate": "10MHz 12bit",
"ZStage-Port": "COM8",
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"CoolsnapHQ-MaskLines": "11",
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"CoolsnapHQ-Port": "Normal",
"SlicePosition": -1,
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"CoolsnapHQ-Gain": "2",
"Exposure-ms": 2000,
"CoolsnapHQ-Description": "PVCAM API device adapter",
"ZStage-Axis": "Z",
"COM7-Description": "Serial port driver (boost:asio)",
"Core-AutoShutter": "1",
"COM7-DelayBetweenCharsMs": "0.0000",
"CoolsnapHQ-Offset": "2593",
"Wheel-A-Busy": "0",
"COM7-Parity": "None",
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"Core-XYStage": "",
"Wheel-B-Label": "Filter-3",
"AxisPositions": null,
"COM8-Parity": "None",
"CoolsnapHQ-PMode": "Normal Parallel Clocking",
"Time": "2012-06-01 10:14:43 -0700",
"CoolsnapHQ-Binning": "1",
"Epi-Port": "COM7",
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"CoolsnapHQ-PVCAM Version": "2.7.6",
"Epi-Name": "Shutter-A 10-2",
"Wheel-B-Busy": "0",
"Core-AutoFocus": "",
"COM7-StopBits": "1",
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"Wheel-B-Name": "Wheel-B",
"COM8-DelayBetweenCharsMs": "0.0000",
"BitDepth": 12,
"Slice": 0,
"CoolsnapHQ-CCDTemperatureSetPoint": "-30",
"Wheel-A-Label": "Filter-4",
"COM8-AnswerTimeout": "500.0000",
"Wheel-B-Description": "Sutter Lambda filter wheel adapter",
"CoolsnapHQ-Exposure": "2000.00",
"ChannelIndex": 1,
"Wheel-B-Port": "COM7",
"Core-Shutter": "Epi",
"COM7-BaudRate": "9600",
"Wheel-A-State": "4",
"UUID": "30bf238d-bd63-4535-bf83-3dcfbc084e68",
"Epi-Description": "Sutter Lambda shutter adapter",
"Core-Camera": "CoolsnapHQ",
"CoolsnapHQ-PostscanPixels": "40",
"Core-TimeoutMs": "5000",
"Core-SLM": "",
"CoolsnapHQ-Trigger Timeout (secs)": "2",
"ZStage-Description": "ASI Z-stage driver adapter",
"ElapsedTime-ms": 3889,
"Wheel-A-Name": "Wheel-A",
"Wheel-B-Speed": "3",
"CoolsnapHQ-TransposeXY": "0",
"CoolsnapHQ-Firmware Version": "2132",
"Wheel-A-Description": "Sutter Lambda filter wheel adapter",
"Frame": 0,
"Wheel-A-Port": "COM7",
"Core-ChannelGroup": "Channel",
"PositionIndex": 0,
"Width": 1392,
"WaitInterval": null,
"PositionName": null,
"PixelSizeUm": 0,
"Height": 1040,
"Summary": {
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"Interval_ms": 0,
"UUID": "775aaa0b-87c9-4142-9586-d508da358802",
"UserName": "cfuller",
"Depth": 2,
"PixelType": "GRAY16",
"Time": "2012-06-01 10:14:40 -0700",
"Date": "2012-06-01",
"z-step_um": 0.25,
"MetadataVersion": 10,
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],
"Width": 1392,
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"ROI": [
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1392,
1040
],
"ChNames": [
"DAPI",
"FITC",
"RHOD"
],
"IJType": 1,
"GridRow": 0,
"Comment": "",
"Height": 1040,
"GridColumn": 0,
"Prefix": "20120601_fiberspreads_flowcell_T",
"PixelSize_um": 0,
"Frames": 0,
"BitDepth": 12,
"KeepShutterOpenChannels": true,
"Source": "Micro-Manager",
"Channels": 3,
"ComputerName": "horntail",
"CustomIntervals_ms": [],
"KeepShutterOpenSlices": false,
"ChColors": [
-16776961,
-16711936,
-65536
],
"TimeFirst": false,
"ChContrastMax": [
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-2147483648,
-2147483648
],
"Positions": 0,
"Directory": "C:\\Documents and Settings\\Colin Fuller/Images"
},
"Source": "CoolsnapHQ",
"Wheel-A-Delay_ms": "0.0000",
"CoolsnapHQ-PrescanPixels": "21",
"CoolsnapHQ-CCDTemperature": "-30",
"COM8-DataBits": "8",
"Epi-Mode": "Fast",
"Binning": "1",
"CoolsnapHQ-OutputTriggerFirstMissing": "0",
"CoolsnapHQ-Y-dimension": "1040",
"Wheel-A-Speed": "3",
"Wheel-B-Delay_ms": "0.0000",
"Epi-State": "1",
"PixelType": "GRAY16",
"COM7-Name": "COM7",
"COM8-StopBits": "1",
"COM7-DataBits": "8",
"COM8-Verbose": "1",
"CoolsnapHQ-FullWellCapacity": "16000",
"YPositionUm": null,
"CoolsnapHQ-ClearCycles": "2",
"XPositionUm": null,
"CoolsnapHQ-Name": "CoolsnapHQ",
"FileName": "img_000000000_FITC_000.tif",
"COM8-Description": "Serial port driver (boost:asio)",
"Core-Galvo": "Undefined",
"COM8-BaudRate": "9600",
"COM8-Handshaking": "Off",
"CameraChannelIndex": 0,
"SliceIndex": 0,
"ZPositionUm": -324.5
},
"FrameKey-0-2-0": {
"Core-Focus": "ZStage",
"Channel": "RHOD",
"Core-Initialize": "1",
"COM7-AnswerTimeout": "500.0000",
"CoolsnapHQ-ShutterMode": "Open Shutter Pre-Exposure",
"COM7-Handshaking": "Off",
"FrameIndex": 0,
"CoolsnapHQ-TransposeMirrorX": "0",
"CoolsnapHQ-TransposeMirrorY": "0",
"Wheel-B-State": "4",
"CoolsnapHQ-ClearMode": "Clear Pre-Exposure",
"CoolsnapHQ-TriggerMode": "Timed",
"Wheel-B-ClosedPosition": "",
"COM8-Name": "COM8",
"ZStage-Name": "ZStage",
"CoolsnapHQ-X-dimension": "1392",
"CoolsnapHQ-ChipName": "ICX285 ",
"CoolsnapHQ-PixelType": "12bit",
"CoolsnapHQ-PreampDelay": "1",
"CoolsnapHQ-PreampOffLimit": "10000",
"CoolsnapHQ-ReadoutRate": "10MHz 12bit",
"ZStage-Port": "COM8",
"Core-ImageProcessor": "",
"CoolsnapHQ-MaskLines": "11",
"CoolsnapHQ-TransposeCorrection": "0",
"CoolsnapHQ-Port": "Normal",
"SlicePosition": -1,
"Wheel-A-ClosedPosition": "",
"CoolsnapHQ-Gain": "2",
"Exposure-ms": 2000,
"CoolsnapHQ-Description": "PVCAM API device adapter",
"ZStage-Axis": "Z",
"COM7-Description": "Serial port driver (boost:asio)",
"Core-AutoShutter": "1",
"COM7-DelayBetweenCharsMs": "0.0000",
"CoolsnapHQ-Offset": "2593",
"Wheel-A-Busy": "0",
"COM7-Parity": "None",
"NextFrame": 0,
"Core-XYStage": "",
"Wheel-B-Label": "Filter-4",
"AxisPositions": null,
"COM8-Parity": "None",
"CoolsnapHQ-PMode": "Normal Parallel Clocking",
"Time": "2012-06-01 10:14:46 -0700",
"CoolsnapHQ-Binning": "1",
"Epi-Port": "COM7",
"COM7-Verbose": "1",
"CoolsnapHQ-PVCAM Version": "2.7.6",
"Epi-Name": "Shutter-A 10-2",
"Wheel-B-Busy": "0",
"Core-AutoFocus": "",
"COM7-StopBits": "1",
"CoolsnapHQ-ActualInterval-ms": "0.0000",
"Wheel-B-Name": "Wheel-B",
"COM8-DelayBetweenCharsMs": "0.0000",
"BitDepth": 12,
"Slice": 0,
"CoolsnapHQ-CCDTemperatureSetPoint": "-30",
"Wheel-A-Label": "Filter-5",
"COM8-AnswerTimeout": "500.0000",
"Wheel-B-Description": "Sutter Lambda filter wheel adapter",
"CoolsnapHQ-Exposure": "2000.00",
"ChannelIndex": 2,
"Wheel-B-Port": "COM7",
"Core-Shutter": "Epi",
"COM7-BaudRate": "9600",
"Wheel-A-State": "5",
"UUID": "7cf28ff0-9a64-4fd3-b9c1-407cb02760c5",
"Epi-Description": "Sutter Lambda shutter adapter",
"Core-Camera": "CoolsnapHQ",
"CoolsnapHQ-PostscanPixels": "40",
"Core-TimeoutMs": "5000",
"Core-SLM": "",
"CoolsnapHQ-Trigger Timeout (secs)": "2",
"ZStage-Description": "ASI Z-stage driver adapter",
"ElapsedTime-ms": 6390,
"Wheel-A-Name": "Wheel-A",
"Wheel-B-Speed": "3",
"CoolsnapHQ-TransposeXY": "0",
"CoolsnapHQ-Firmware Version": "2132",
"Wheel-A-Description": "Sutter Lambda filter wheel adapter",
"Frame": 0,
"Wheel-A-Port": "COM7",
"Core-ChannelGroup": "Channel",
"PositionIndex": 0,
"Width": 1392,
"WaitInterval": null,
"PositionName": null,
"PixelSizeUm": 0,
"Height": 1040,
"Summary": {
"Slices": 9,
"Interval_ms": 0,
"UUID": "775aaa0b-87c9-4142-9586-d508da358802",
"UserName": "cfuller",
"Depth": 2,
"PixelType": "GRAY16",
"Time": "2012-06-01 10:14:40 -0700",
"Date": "2012-06-01",
"z-step_um": 0.25,
"MetadataVersion": 10,
"PositionIndex": 0,
"SlicesFirst": false,
"ChContrastMin": [
2147483647,
2147483647,
2147483647
],
"Width": 1392,
"PixelAspect": 1,
"MicroManagerVersion": "1.4.10",
"ROI": [
0,
0,
1392,
1040
],
"ChNames": [
"DAPI",
"FITC",
"RHOD"
],
"IJType": 1,
"GridRow": 0,
"Comment": "",
"Height": 1040,
"GridColumn": 0,
"Prefix": "20120601_fiberspreads_flowcell_T",
"PixelSize_um": 0,
"Frames": 0,
"BitDepth": 12,
"KeepShutterOpenChannels": true,
"Source": "Micro-Manager",
"Channels": 3,
"ComputerName": "horntail",
"CustomIntervals_ms": [],
"KeepShutterOpenSlices": false,
"ChColors": [
-16776961,
-16711936,
-65536
],
"TimeFirst": false,
"ChContrastMax": [
-2147483648,
-2147483648,
-2147483648
],
"Positions": 0,
"Directory": "C:\\Documents and Settings\\Colin Fuller/Images"
},
"Source": "CoolsnapHQ",
"Wheel-A-Delay_ms": "0.0000",
"CoolsnapHQ-PrescanPixels": "21",
"CoolsnapHQ-CCDTemperature": "-30",
"COM8-DataBits": "8",
"Epi-Mode": "Fast",
"Binning": "1",
"CoolsnapHQ-OutputTriggerFirstMissing": "0",
"CoolsnapHQ-Y-dimension": "1040",
"Wheel-A-Speed": "3",
"Wheel-B-Delay_ms": "0.0000",
"Epi-State": "0",
"PixelType": "GRAY16",
"COM7-Name": "COM7",
"COM8-StopBits": "1",
"COM7-DataBits": "8",
"COM8-Verbose": "1",
"CoolsnapHQ-FullWellCapacity": "16000",
"YPositionUm": null,
"CoolsnapHQ-ClearCycles": "2",
"XPositionUm": null,
"CoolsnapHQ-Name": "CoolsnapHQ",
"FileName": "img_000000000_RHOD_000.tif",
"COM8-Description": "Serial port driver (boost:asio)",
"Core-Galvo": "Undefined",
"COM8-BaudRate": "9600",
"COM8-Handshaking": "Off",
"CameraChannelIndex": 0,
"SliceIndex": 0,
"ZPositionUm": -324.5
},
"FrameKey-0-0-1": {
"Core-Focus": "ZStage",
"Channel": "DAPI",
"Core-Initialize": "1",
"COM7-AnswerTimeout": "500.0000",
"CoolsnapHQ-ShutterMode": "Open Shutter Pre-Exposure",
"COM7-Handshaking": "Off",
"FrameIndex": 0,
"CoolsnapHQ-TransposeMirrorX": "0",
"CoolsnapHQ-TransposeMirrorY": "0",
"Wheel-B-State": "2",
"CoolsnapHQ-ClearMode": "Clear Pre-Exposure",
"CoolsnapHQ-TriggerMode": "Timed",
"Wheel-B-ClosedPosition": "",
"COM8-Name": "COM8",
"ZStage-Name": "ZStage",
"CoolsnapHQ-X-dimension": "1392",
"CoolsnapHQ-ChipName": "ICX285 ",
"CoolsnapHQ-PixelType": "12bit",
"CoolsnapHQ-PreampDelay": "1",
"CoolsnapHQ-PreampOffLimit": "10000",
"CoolsnapHQ-ReadoutRate": "10MHz 12bit",
"ZStage-Port": "COM8",
"Core-ImageProcessor": "",
"CoolsnapHQ-MaskLines": "11",
"CoolsnapHQ-TransposeCorrection": "0",
"CoolsnapHQ-Port": "Normal",
"SlicePosition": -0.75,
"Wheel-A-ClosedPosition": "",
"CoolsnapHQ-Gain": "2",
"Exposure-ms": 500,
"CoolsnapHQ-Description": "PVCAM API device adapter",
"ZStage-Axis": "Z",
"COM7-Description": "Serial port driver (boost:asio)",
"Core-AutoShutter": "1",
"COM7-DelayBetweenCharsMs": "0.0000",
"CoolsnapHQ-Offset": "2593",
"Wheel-A-Busy": "0",
"COM7-Parity": "None",
"NextFrame": 0,
"Core-XYStage": "",
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"Epi-Description": "Sutter Lambda shutter adapter",
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"ZStage-Description": "ASI Z-stage driver adapter",
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"Wheel-A-Name": "Wheel-A",
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"Wheel-A-Description": "Sutter Lambda filter wheel adapter",
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"Width": 1392,
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"Summary": {
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"Time": "2012-06-01 10:14:40 -0700",
"Date": "2012-06-01",
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"ChNames": [
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"Positions": 0,
"Directory": "C:\\Documents and Settings\\Colin Fuller/Images"
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"CoolsnapHQ-Name": "CoolsnapHQ",
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"COM8-Description": "Serial port driver (boost:asio)",
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"COM8-Handshaking": "Off",
"CameraChannelIndex": 0,
"SliceIndex": 8,
"ZPositionUm": -322.5
}
}
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