QPTIFF Channels

	A	B	D	E	F	H	I	J	K
1		The following fields are required to be the first four columns in the *.qptiff.channels.csv file (order matters). Data providers are welcome to include additional columns that further describe the channels. This file should include one row per channel in the accompanying QPTIFF file.
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5	Field Name	Field Type	Definition	Options: required, optional	NOTES	VALUES for CATEGORICAL FIELDS
6	Field Name	Field Type	Definition	Options: required, optional	NOTES	is channel used for nuclei segmentation	is channel used for cell segmentation	is antibody	channel quality

7	channel id	text	Structure of the identifier depends on the acquisition system. Whenever possible this should exactly match the channel ID in the QPTIFF file. For example the channel ID in an QPTIFF might be something like "Channel:0:13" which would then be the value entered here.	required		Yes	Yes	Yes	good
8	is channel used for nuclei segmentation	boolean	Specifies if this channel can be used by algorithms performing nuclei segmentation ("Yes" or "No").	required	In data types for which a HIVE pipeline performs cell and nuclear segmentation, exactly one channel must have value "Yes".	No	No	No	fair
9	is channel used for cell segmentation	boolean	Specifies if this channel can be used by algorithms performing cell segmentation ("Yes" or "No").	required	In data types for which a HIVE pipeline performs cell and nuclear segmentation, exactly one channel must have value "Yes".	Not applicable	Not applicable	Not applicable	poor
10	is antibody	boolean	Does this channel encode image intensities associated with an antibody ("Yes" or "No")? If "Yes" then the relevant antibody is expected to be listed in the antibodies.tsv file with the same channel ID.	required
11	channel quality	categorical	This is a rough metric of the quality of the individual channel within the image. If any channels are denoted as "poor" quality, then the reason for including the poor channel(s) must be noted in the abstract for this dataset.	optional
12	default for display	boolean	This denotes if this channel should be enabled by default in the data portal visuals.	optional
13	threshold	integer	This denotes the maximum threshold value for this channel when being displayed	optional
14	minimum threshold	integer	This denotes the minimum threshold value for this channel when being displayed.	optional
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