top bar

Files and Metadata

Micro-Manager's default image data sets are in single-plane TIFF images with an accompanying metadata.txt file.

1.4 (MetadataVersion 10, subject to change)

The metadata.txt file contains a JSON key-value map. This version is supposed to be readable from Micro-Manager 1.3. The first key is "Summary". Here is an example (object keys sorted for clarity):

"Summary": {
  "Channels": 3,
  "ChColors": [-3342592, -13382401, -39220],
  "ChContrastMax": [-2147483648, -2147483648, -2147483648],
  "ChContrastMin": [2147483647, 2147483647, 2147483647],
  "ChNames": ["DAPI", "FITC", "Rhodamine"],
  "Comment": "",
  "ComputerName": "udp011420uds.ucsf.edu",
  "Date": "2011-01-18",
  "Depth": 1,
  "Directory": "/Users/arthur/AcquisitionData",
  "Frames": 7,
  "GridColumn": 0,
  "GridRow": 0,
  "Height": 512,
  "IJType": 0,
  "Interval_ms": 0,
  "KeepShutterOpenChannels": false,
  "KeepShutterOpenSlices": false,
  "MetadataVersion": 10,
  "PixelAspect": 1,
  "PixelSize_um": 1,
  "PixelType": "GRAY8",
  "PositionIndex": 0,
  "Positions": 2,
  "Prefix": "Untitled",
  "Slices": 5,
  "SlicesFirst": true,
  "Source": "Micro-Manager",
  "Time": "2011-01-18 Tue 16:52:41 -0800",
  "TimeFirst": false,
  "UserName": "arthur",
  "UUID": "e47de3d2-8439-4559-9ffb-3368273b2ed5",
  "Width": 512,
  "z-step_um": 1,
},

(More keys will likely be added to this Summary.)

Following this are a series of "FrameKey" key-value pairs, in the order in which they were acquired (and roughly in the order they are displayed). Each FrameKey contains a number of Acquisition and Image keys, a "Summary" key (as above) as well as all properties of the System when each image was acquired (sorted here for clarity):

"FrameKey-0-0-0": {
  "Autofocus-Description": "Demo auto-focus adapter",
  "Autofocus-Name": "DAutoFocus",
  "AxisPositions": null,
  "Binning": "1",
  "Camera-Binning": "1",
  "Camera-BitDepth": "8",
  "Camera-CameraID": "V1.0",
  "Camera-CameraName": "DemoCamera-MultiMode",
  "Camera-CCDTemperature": "0.0000",
  "Camera-Description": "Demo Camera Device Adapter",
  "Camera-ErrorSimulation": "0",
  "Camera-Exposure": "10.00"
  "Camera-Gain": "0",
  "Camera-Name": "DCam",
  "Camera-Offset": "0",
  "Camera-OnCameraCCDXSize": "512",
  "Camera-OnCameraCCDYSize": "512",
  "Camera-PixelType": "8bit",
  "Camera-PropertyRefreshSimulation": "0",
  "Camera-ReadoutTime": "0.0000",
  "Camera-ScanMode": "1",
  "Camera-TestProperty1": "0.0000",
  "Camera-TestProperty2": "0.0000",
  "Camera-TestProperty3": "0.0000",
  "Camera-TestProperty4": "0.0000",
  "Camera-TransposeCorrection": "0",
  "Camera-TransposeMirrorX": "0",
  "Camera-TransposeMirrorY": "0",
  "Camera-TransposeXY": "0",
  "Channel": "DAPI",
  "ChannelIndex": 0,
  "Core-AutoFocus": "Autofocus",
  "Core-AutoShutter": "1",
  "Core-Camera": "Camera",
  "Core-ChannelGroup": "Channel",
  "Core-Focus": "Z",
  "Core-ImageProcessor": "",
  "Core-Initialize": "1",
  "Core-Shutter": "Shutter",
  "Core-SLM": "",
  "Core-TimeoutMs": "5000",
  "Core-XYStage": "XY",
  "Dichroic-ClosedPosition": "0",
  "Dichroic-Description": "Demo filter wheel driver",
  "Dichroic-Label": "400DCLP",
  "Dichroic-Name": "DWheel",
  "Dichroic-State": "0",
  "ElapsedTime-ms": 301,
  "Emission-ClosedPosition": "0",
  "Emission-Description": "Demo filter wheel driver",
  "Emission-Label": "Chroma-HQ620",
  "Emission-Name": "DWheel",
  "Emission-State": "0",
  "Excitation-ClosedPosition": "0",
  "Excitation-Description": "Demo filter wheel driver",
  "Excitation-Label": "Chroma-D360",
  "Excitation-Name": "DWheel",
  "Excitation-State": "0",
  "Exposure-ms": 10,
  "FileName": "img_000000000_DAPI_000.tif",
  "Frame": 0,
  "Height": 512,
  "Objective-Description": "Demo objective turret driver",
  "Objective-Label": "Nikon 10X S Fluor",
  "Objective-Name": "DObjective",
  "Objective-State": "1",
  "Path-Description": "Demo light-path driver",
  "Path-Label": "State-0",
  "Path-Name": "DLightPath",
  "Path-State": "0",
  "PixelSizeUm": 1,
  "PixelType": "GRAY8",
  "PositionIndex": 0,
  "PositionName": "Pos0",
  "Shutter-Description": "Demo shutter driver",
  "Shutter-Name": "DShutter",
  "Shutter-State": "0",
  "Slice": 0,
  "SlicePosition": 0,
  "Source": "Camera",
  "Summary": {...},
  "Time": "2011-01-18 Tue 16:52:41 -0800",
  "UUID": "03341ef4-ccb1-4d84-9c1d-7db295e7fd99",
  "Width": 512,
  "XY-Description": "Demo XY stage driver",
  "XY-Name": "DXYStage",
  "XY-TransposeMirrorX": "0",
  "XY-TransposeMirrorY": "0",
  "Z-Description": "Demo stage driver",
  "Z-Name": "DStage",
  "Z-Position": "0.0000",
  "ZPositionUm": 0
 },

In addition, these FrameKeys are also stored as metadata in the image tiff files.

1.3 (MetadataVersion 8)

The metadata.txt file contains a JSON key-value map. Keys are generally in random order. Most keys in this map are "FrameKey-(Frame)-(Channel)-(Slice)" for each image.

Here is an example of a FrameKey:

   "FrameKey-3-1-1": {
      "Exposure-ms": "10.0",
      "Time": "Tue Oct 12 09:38:26 PDT 2010",
      "ElapsedTime-ms": 474,
      "Slice": 1,
      "Channel": "DAPI",
      "FileName": "img_000000003_DAPI_001.tif",
      "Y-um": "-0.0",
      "X-um": "-0.0",
      "Z-um": "0.0",
      "Frame": 3
   }

Also in the root map is a "SystemState" key (not found in later versions of Micro-Manager), which provides the state of the system for each image:

 "SystemState": {
      "FrameKey-3-1-1": {
         "Camera-TransposeMirrorX": "0",
         "Core-AutoFocus": "Autofocus",
         "Camera-Name": "DCam",
         "Objective-Label": "Nikon 10X S Fluor",
         "Dichroic-State": "0",
         "Dichroic-Label": "400DCLP",
         "Dichroic-Name": "DWheel",
         "Camera-ErrorSimulation": "0",
         "Camera-ReadoutTime": "0.0000",
         "Camera-TestProperty3": "3.0470",
         "Camera-TransposeCorrection": "0",
         "Autofocus-Name": "DAutoFocus",
         "XY-Description": "Demo XY stage driver",
         "Core-Focus": "Z",
         "Camera-Gain": "0",
         "Objective-Name": "DObjective",
         "Core-TimeoutMs": "5000",
         "Camera-Offset": "0",
         "Emission-ClosedPosition": "0",
         "Core-XYStage": "XY",
         "Camera-TestProperty4": "4.6789",
         "Emission-Name": "DWheel",
         "Core-ChannelGroup": "Channel",
         "Z-Name": "DStage",
         "Z-Position": "0.0000",
         "Excitation-ClosedPosition": "0",
         "Shutter-Description": "Demo shutter driver",
         "Z-Description": "Demo stage driver",
         "Camera-TransposeXY": "0",
         "Emission-Description": "Demo filter wheel driver",
         "Core-AutoShutter": "1",
         "Excitation-Label": "Chroma-D360",
         "Objective-State": "1",
         "XY-TransposeMirrorX": "0",
         "Camera-CameraName": "DemoCamera-MultiMode",
         "Core-Camera": "Camera",
         "Excitation-Description": "Demo filter wheel driver",
         "Objective-Description": "Demo objective turret driver",
         "Camera-TestProperty1": "1.5328",
         "Excitation-State": "0",
         "Shutter-Name": "DShutter",
         "Camera-TransposeMirrorY": "0",
         "Camera-CameraID": "V1.0",
         "Path-Name": "DLightPath",
         "Camera-Binning": "1",
         "Camera-ScanMode": "1",
         "Camera-Description": "Demo Camera Device Adapter",
         "Core-Shutter": "Shutter",
         "Autofocus-Description": "Demo auto-focus adapter",
         "Shutter-State": "0",
         "XY-TransposeMirrorY": "0",
         "Excitation-Name": "DWheel",
         "Path-Label": "State-0",
         "Camera-Exposure": "10.00",
         "Dichroic-ClosedPosition": "0",
         "Camera-CCDTemperature": "0.0000",
         "Camera-PixelType": "8bit",
         "Core-Initialize": "1",
         "Camera-TestProperty2": "2.2190",
         "Core-SLM": "",
         "Core-ImageProcessor": "",
         "Emission-Label": "Chroma-HQ620",
         "XY-Name": "DXYStage",
         "Camera-BitDepth": "8",
         "Emission-State": "0",
         "Dichroic-Description": "Demo filter wheel driver",
         "Path-State": "0",
         "Path-Description": "Demo light-path driver"
      },

There is also a "Summary" key mapped to a nested JSON data structure, such as this one:

"Summary": {
      "z-step_um": "1.0",
      "Time": "2010-10-12 09:38:25",
      "Comment": "",
      "Height": 512,
      "Date": "2010-10-12",
      "Channels": 4,
      "PixelAspect": "1.0",
      "GUID": "e99541d7b6c27820-32c4303b5f03f7ca",
      "ChColors": [
         -16724941,
         -65485,
         -16776961,
         -6749953
      ],
      "Width": 512,
      "IJType": 0,
      "Interval_ms": 1,
      "ChNames": [
         "Cy5",
         "DAPI",
         "FITC",
         "Rhodamine"
      ],
      "GridRow": "0",
      "UserName": "arthur",
      "Depth": 1,
      "GridColumn": "0",
      "ChContrastMax": [
         22,
         22,
         22,
         22
      ],
      "PixelSize_um": "1.0",
      "Source": "Micro-Manager",
      "Slices": 2,
      "MetadataVersion": 8,
      "ComputerName": "udp011420uds.ucsf.edu",
      "Frames": 5,
      "Position": "Pos0",
      "ChContrastMin": [
         2,
         2,
         2,
         2
      ]
   },
© Micro-Manager : Vale Lab, UCSF 2006-2011 | All Rights Reserved | Contact