Extra-Cell ROI Data table
Requirement level: optional
Recommended: Yes
Namespace: 4dn_FOF-CT_extracell
Summary
This table is optionally used to document properties (i.e., volume, mean fluorescence intensity) that are globally associated with individual extracellular structures (e.g., Tissue, Organoid, etc.) Regions of Interest (ROI) identified as part of this experiment.
These are properties that are shared by all bright Spots, Traces and Cells
that belong to an individual extracellular structure identified as part of
this study. Each row in the table corresponds to a different extracellular structure studied in the experiment and is identified by a unique Extra_Cell_ROI_ID that links the data reported in this table with data stored in one of the other tables (e.g., DNA-Spot/Trace Data core table, RNA Spot Data table, etc.).
As such, this table is mandatorily indexed by Extra_Cell_ROI_ID.
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_extracell.
Tip
If applicable, 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.
Tip
The table MUST contain at least 1 Optional Column.
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_extracell |
|
##Extra_Cell_ROI_Type= |
This field records the type of extracellular structure ROIs reported in this table. It is recommended to use an ontology term such as a child of the EFO ‘organism part’ term. Examples include: Tissue, Organoid, etc. |
Tissue |
|
##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 |
Conditional requirement: this MUST be reported if any locations metrics are reported. |
##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 in this table. |
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 |
Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. |
#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 |
Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. |
#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 |
Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. |
#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 |
Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. |
#Software_Repository: |
The URL of any repository or archive where the Software executable release can be obtained. |
Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. |
|
#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,. |
Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. |
|
#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. |
Spot 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_quality, 4dn_FOF-CT_bio, 4dn_FOF-CT_trace |
|
##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. |
(Extra_Cell_ROI_ID, Optional_Column_1, Optional_Column_2, Optional_Colummn_3) |
Data Columns
For full instructions see Data Columns
Each row corresponds to data associated with an individual extracellular ROI.
The first column of this table is always Extra_Cell_ROI_ID.
This table MUST contain at least 1 Optional Column.
The order of the other columns is at user’s discretion.
The order of the rows is at user’s discretion.
Name |
Description |
Example |
Conditional requirement conditions |
|---|---|---|---|
Extra_Cell_ROI_ID |
This fields reports the unique identifier for an extracellular structure (e.g. Tissue; Organoid) Region of Interest (ROI) identified as part of this experiment. Note: this is used to connect individual Cells that are part of the same extracellular ROI. |
1 |
|
Optional_Column_1 |
|||
Optional_Column_2 |
|||
Optional_Column_3 |
Example
The only mandatory column in this table is Extra_Cell_ROI_ID. 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 the user is reporting the number of specific cells are detected within individual extracellular ROIs as well as the volume of each ROI.
##FOF-CT_Version=v1.0
##Table_Namespace=4dn_FOF-CT_extracell
##Extra_Cell_ROI_Type=Organoid
##XYZ_Unit=micron
#Lab_Name: Nobel
#Experimenter_Name: John Doe
#Cxperimenter_Contact: john.doe@email.com
#Description: In this experiment organoids were identified by segmentation using the indicated algorithm on the basis of bright field signal.
#Software_Title: AlgorithmXYZ
#Software_Type: Segmentation
#Software_Authors: John Doe
#Software_Description: A pretty clear description
#Software_Repository: https://github.com/repo_name_goes_here
#Software_PreferredCitationID: https://doi.org/doi_goes_here
#^Cell_A_nr: the number of identified Cells of type A identified to belong to this extracellular ROI.
#^Cell_B_nr: the number of identified Cells of type B identified to belong to this extracellular ROI.
#^ROI_Volume: the volume of this extracellular ROI expressed in micron^3.
#Additional_Tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace
##Columns=(Extra_Cell_ROI, Cell_A_nr, Cell_B_nr, ROI_Volume)
1, 10, 22, 13453
2, 0, 11, 35545
3, 10, 33, 10010
4, 44, 0, 25340