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
]
},