Spot Demultiplexing table
Requirement level: optional
Recommended: Yes
Namespace: 4dn_FOF-CT_demultiplexing
Summary
This table is optional and is designed to be used in the case of multiplexed FISH experiments (i.e., MERFISH) in which the final localization of a bright DNA or RNA Spot results from the combination of multiple individual localization events (e.g., by combining particles detected and localized in separate images).
In such a case the final Spot localization data is recorded in the DNA-Spot/Trace Data core table, while the underlying primary localization data can be recorded by using this table, as shown for DNA Spots in the example below.
This table is indexed by Loc_ID, mandatorily reports the X, Y, Z coordinates of the Localization event and the fluorescent channel (Fluor) in which this localization was detected. In addition, the table has a mandatory Spot_ID column that is used to link individual localization events to the resulting Spot.
Other columns are at user’s discretion.
Warning
All MANDATORY header fields and column names are indicated in bold. All conditionally required header fields and column names are indicated in italics.
File Header
For full instructions see File Header
The first line in the header is always
##FOF-CT_Version=vX.X.The second line in the header is always
##Table_Namespace=4dn_FOF-CT_mapping.
Tip
The header MUST contain a mandatory set of fields that describe any Software tool that was used to produce/process data in this table. If more than one software tool was used, please repeat a set of Software-fields for describing each of them.
The header MUST include a detailed description of each optional columns used.
Name |
Description |
Example |
Conditional requirement conditions |
|---|---|---|---|
##FOF-CT_Version= |
Version of the FOF format used in this case. |
v1.0 |
|
##Table_Namespace= |
Identifier for this type of table. Value must be as in the example. |
4dn_FOF-CT_demultiplexing |
|
##XYZ_Unit= |
If relevant, the unit used to represent XYZ locations or distances in this table. Note: use micron to avoid problem with special, Greek symbols. Other allowed values should be drawn from SI units of Length. Examples: ‘nm’, ‘micron’ ‘mm’ etc. |
micron |
|
##Time_Unit= |
If relevant, the unit used to represent a time interval in this table. Allowed values should be drawn from SI units of Time or be one of the following: ‘min’, and ‘hr’. |
sec |
Conditional requirement: this MUST be reported if any time metrics are reported. |
##Intensity_Unit= |
If relevant, the unit used to represent intensity measurements. |
a.u. |
Conditional requirement: this MUST be reported if any intensity metrics are reported. |
#Lab_Name: |
name of the lab where the experiment was performed. |
Nobel |
|
#Experimenter_Name: |
name of the person performing the experiment. |
John Doe |
|
#Experimenter_Contact: |
email address of the person performing the experiment. |
||
#Description: |
A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility. |
||
#Software_Title: |
The name of the Software tool that was used to produce the results reported in this table. If more than one software tool was used, please repeat a set of Software-fields for describing each of them. |
AlgorithmXYZ |
|
#Software_Type: |
The type of this Software used to produce results recorded in this table. Allowed values: SpotLoc, Tracing, SpotLoc+Tracing, Segmentation, QC, Other |
Segmentation |
|
#Software_Authors: |
The Name(s) of the individual Author(s) of this Software. In case there are more than one Authors, individual names should be listed as follows, Doe, John; Smith, Jane; etc,. |
John Doe |
|
#Software_Description: |
A free-text, description of this Software. This description should provide a detailed understanding of the algortithm and of the analysis parameters that were used, in order to guarantee interpretation and reproducibility. |
A pretty clear description |
|
#Software_Repository: |
The URL of any repository or archive where the Software executable release can be obtained. |
||
#Software_PreferredCitationID: |
The Unique Identifier for the preferred/primary publication describing this Software. Examples include, Digital Object Identifier (DOI), PubMed Central Identifier (PMCID), ArXiv.org ID etc,. |
||
#Intensity_Measurement_Method: |
If relevant, the method that was used to perform intensity measurements. In particular, sufficient information should be provided to document how digital intensity signals were converted to Photon counts. |
Localization centroid intensity |
Conditional requirement: this MUST be reported if any intensity metrics are reported. |
#^Optional_Column_1: |
Optional column 1 description. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility. |
||
#^Optional_Column_2: |
Optional column 2 description. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility. |
||
#^Optional_Column_3: |
Optional column 3 description. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility. |
||
#Additional_Tables: |
list of the additional tables being submitted. Note: use a comma to separate each table name from the next. |
4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_bio, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell |
|
##Columns= |
list of the data column headers used in the table. Note: enclose the column headers and use a comma to separate each header name from the next. |
(Spot_ID, Loc_ID, X, Y, Z, Fluor) |
Data Columns
For full instructions see Data Columns
This table is indexed by Loc_ID and therefore each row corresponds to data associated with an individual Localization event.
The first columns are always: Loc_ID, Spot_ID, X, Y, Z, Fluor.
The content and order of all other columns is at user’s discretion.
The order of the rows is at user’s discretion.
Name |
Description |
Example |
Conditional requirement conditions |
|---|---|---|---|
Loc_ID |
A unique identifier for this individual Localization event. |
1 |
|
Spot_ID |
A unique identifier for the bright DNA or RNA Spot with which this individual localization event is associated. |
1 |
|
X |
The sub-pixel X coordinate of this Localization event. |
14.43 |
|
Y |
The sub-pixel Y coordinate of this Localization event. |
41.43 |
|
Z |
The sub-pixel Z coordinate of this Localization event. |
1.23 |
|
Fluor |
the fluorescent channel in which this localization was detected |
||
Optional_Column_1 |
|||
Optional_Column_2 |
|||
Optional_Column_3 |
Example
The only mandatory columns in this table are Loc_ID, Spot_ID, X, Y, Z, Fluor. All other columns are optional and must be defined by the user using a Header line starting with #^.
Tip
The optional columns in this example table are included for illustrative purposes only and describe a case in which DNA spots are detected with multiplexed barcodes.
##FOF-CT_Version=v1.0
##Table_Namespace=4dn_FOF-CT_demultiplexing
##XYZ_Unit=micron
#Lab_Name: Nobel
#Experimenter_Name: John Doe
#Experimenter_Contact: john.doe@email.com
#Description: This table reports the localization events that were associated with each identified birght DNA Spot
#Software_Title: BestLocalizationSoftware
#Software_Type: Loc
#Software_Authors: Doe, J.
#Software_Description: A pretty clear description
#Software_Repository: https://github.com/repo_name_goes_here
#Software_PreferredCitationID: https://doi.org/doi_goes_here
#Intensity_Measurement_Method: Localization centroid intensity
#^Hyb: the labeling round in which this localization occurred
#^Fluor: the fluorescent channel in which this localization was detected
#^Brightness: the photon count for this localization event
#^Fit_Quality: the quality of fit for this localization, on a relative scale of 0-1
#Additional_Tables: 4dn_FOF-CT_core, 4dn_FOF-CT_quality
##Columns=(Loc_ID, Spot_ID, X, Y, Z, Hyb, Fluor, Brightness, Fit_Quality)
1, 1, 2342, 2354, 545, 2, cy3, 1003, 0.83
2, 1, 2342, 2354, 545, 2, cy5, 2000, 0.93
3, 1, 2342, 2354, 545, 3, cy5, 1233, 0.85
4, 2, 3345, 5432, 654, 3, cy3, 2324, 0.95
5, 2, 3345, 5432, 654, 3, cy5, 2324, 0.95
6, NA, 4345, 432, 100, 4, cy3, 2324, 0.95
7, 2, 3345, 5432, 654, 4, cy3, 2324, 0.95