[ome-users] bio-formats Micromanager reader issue
Colin Fuller
cjfuller at gmail.com
Sun Jun 3 20:43:47 BST 2012
Hi, Melissa,
I tried updating loci_tools.jar to the latest version and that didn't help,
but I did track it down to a different plugin that I had manually
installed, which included some of the bio-formats image reading classes
from an older version, which were apparently being used instead of those in
loci_tools.jar. I removed the other plugin and now things are working with
the latest build.
Apologies for the trouble and thanks!
Colin
On Sat, Jun 2, 2012 at 5:09 PM, Melissa Linkert <melissa at glencoesoftware.com
> wrote:
> Hi Colin,
>
> > 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.
> *snip*
> > 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
>
> Thank you for the bug report.
>
> I wasn't able to duplicate this error message using the very latest
> trunk build, or the latest version that is in the Fiji updater (and in
> fact, I do recall fixing this very bug a while back).
>
> Could you please run the Fiji updater ("Help > Update Fiji", making sure
> to update "plugins/loci_tools.jar"), restart Fiji, and then see if the
> file opens correctly?
>
> Regards,
> -Melissa
>
> On Fri, Jun 01, 2012 at 03:37:54PM -0700, Colin Fuller wrote:
> > 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
>
> > {
> > "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)",
> > "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-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",
> > "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-2",
> > "COM8-AnswerTimeout": "500.0000",
> > "Wheel-B-Description": "Sutter Lambda filter wheel adapter",
> > "CoolsnapHQ-Exposure": "500.00",
> > "ChannelIndex": 0,
> > "Wheel-B-Port": "COM7",
> > "Core-Shutter": "Epi",
> > "COM7-BaudRate": "9600",
> > "Wheel-A-State": "2",
> > "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,
> > "Width": 1392,
> > "WaitInterval": 0,
> > "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": "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_DAPI_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-0-1-0": {
> > "Core-Focus": "ZStage",
> > "Channel": "FITC",
> > "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": "3",
> > "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-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",
> > "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-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": {
> > "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": "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,
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> > "Wheel-A-Busy": "0",
> > "COM7-Parity": "None",
> > "NextFrame": 0,
> > "Core-XYStage": "",
> > "Wheel-B-Label": "Filter-3",
> > "AxisPositions": null,
> > "COM8-Parity": "None",
> > "CoolsnapHQ-PMode": "Normal Parallel Clocking",
> > "Time": "2012-06-01 10:15:36 -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": 8,
> > "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": "3070388e-7e68-497b-b48c-9850d6ab1314",
> > "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": 57145,
> > "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": "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_008.tif",
> > "COM8-Description": "Serial port driver (boost:asio)",
> > "Core-Galvo": "Undefined",
> > "COM8-BaudRate": "9600",
> > "COM8-Handshaking": "Off",
> > "CameraChannelIndex": 0,
> > "SliceIndex": 8,
> > "ZPositionUm": -322.5
> > },
> > "FrameKey-0-2-8": {
> > "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": null,
> > "Core-XYStage": "",
> > "Wheel-B-Label": "Filter-4",
> > "AxisPositions": null,
> > "COM8-Parity": "None",
> > "CoolsnapHQ-PMode": "Normal Parallel Clocking",
> > "Time": "2012-06-01 10:15:39 -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": 8,
> > "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": "e96fbf0d-3a65-4ca2-9b05-aa072ec2c144",
> > "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": 59562,
> > "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_008.tif",
> > "COM8-Description": "Serial port driver (boost:asio)",
> > "Core-Galvo": "Undefined",
> > "COM8-BaudRate": "9600",
> > "COM8-Handshaking": "Off",
> > "CameraChannelIndex": 0,
> > "SliceIndex": 8,
> > "ZPositionUm": -322.5
> > }
> > }
>
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
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