Metadata.md

@@ -19,15 +19,20 @@ attrib = jsondecode(attrib);  %Convert JSON to struct
 
 The file attributes contain information necessary to initialize pointers to the picture. The attributes contains the following fields:
 
-* ```bitsPerComponentInMemory`` - Number of bits to hold each component (channel)
-* ```bitsPerComponentInMemory`` - Number of bits to hold each component (channel)
-* ```bitsPerComponentInMemory`` - Number of bits to hold each component (channel)
-* ```bitsPerComponentInMemory`` - Number of bits to hold each component (channel)
-* ```bitsPerComponentInMemory`` - Number of bits to hold each component (channel)
-* ```bitsPerComponentInMemory`` - Number of bits to hold each component (channel)
-
-
-
+* ``bitsPerComponentInMemory`` - Number of bits to hold each component (channel)
+* ``bitsPerComponentSignificant`` - Number of bits actually used by each component (channel)
+* ``componentCount`` - Number of channels
+* ``compressionLevel`` - (optional) Level of compression, if used
+* ``compressionType`` - (optional) Type of compression: ``lossless`` or ``lossy``
+* ``heightPx`` - Height of image in pixels
+* ``pixelDataType`` - ``unsigned`` (integer) or ``float`` (double)
+* ``sequenceCount`` - Number of images in the file
+* ``tileHeightPx`` - (optional) Suggested tile height if saved as tiled
+* ``tileWidthPx`` - (optional) Suggested tile width if saved as tiled
+* ``widthBytes`` - Number of bytes from beginning of one line to the next
+* ``widthPx`` - Width of image in pixels
+
+The size of memory needed for an image is ``widthBytes`` * ``heightPx`` * ``componentCount`` * 2 (factor of 2 assuming 16-bit integers).
 
 ## Experiment metadata
 
@@ -57,22 +62,25 @@ File has 19 timepoints and 35 XY locations.
 |  35     |   1            |  'XYPosLoop'  |
 
 
-
-On a file with the following metadata nesting orders:
+In a file with the following metadata nesting orders:
 ```
 TimeLoop - 0
 XYPos - 1
 ```
 coordinates of [10, 0] gives XY = 1, and T = 11;
 
-
-
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+## File metadata
+
+This metadata seems to be mostly related to microscope settings. The data is split into two main fields.
+
+* ``contents``
+  * ``channelCount`` - Number of channels across all frames
+  * ``frameCount`` - Total number of images in the file
+* ``channels``
+  * ``channel``
+    * ``name`` of the channel (set in the optical configuration in Nikon Elements)
+    * ``index`` position of the channel
+    * ``colorRGB`` RGB color to display the channel in
+  * ``loops``
+  * ``microscope`` containing microscope settings
+  * ``volume`` containing information about the position
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