Cell/ROI Mapping table
Requirement level: conditionally required
Namespace: 4dn_FOF-CT_mapping
Summary
This table is used to provide the boundaries of Cells and other ROIs identified as part of this experiment, and it is required in case Cell and other ROI segmentation data were collected as part of this experiment.
This table is conditionally required in case a Sub-Cell ROI Data table, Cell Data table, and/or Extra-Cell ROI Data table tables are deposited with this submission.
The table is organized on a Cell or ROI basis via a Cell or ROI ID and is designed to provide the boundaries of each Cell and ROI boundaries in global coordinates.
This could be done as specified by the OME ROI data model. Alternatively, Cell or ROI boundaries could be provided using 3D MESH models (e.g., using the OBJ format). Additional formats are also allowed.
As such, this table is mandatorily indexed by one of the following Cell_ID, Sub_Cell_ROI_ID or Extra_Cell_ROI_ID.
In addition, the header of the file MUST include the ##ROI_boundaries_format= field to report the format that is used to record the boundaries of the ROI in global coordinates.
As an example, this table might be organized in one of the following manner:
- 1) Cell boundaries
##ROI_boundaries_format=Cell boundaries are reported in global coordinates following the OME Data Model for Polygon - ROI. As such Cell boundaries are defined as lists of comma separated x,y coordinates separated by spaces like “x1,y1 x2,y2 x3,y3” (e.g. “0,0 1,2 3,5”).
|
|
|---|---|
0001 |
“0,0 1,2 3,5” |
- 2) Sub-Cell ROI boundaries
##ROI_boundaries_format=Sub-cell ROI boundaries are reported in global coordinates following the OME Data Model for Polygon - ROI. As such the Cell boundaries are defined as lists of comma separated x,y,z coordinates separated by spaces like “x1,y1,z1 x2,y2,z2 x3,y3,z3” (e.g. “0,0 1,2 3,5”).
|
|
|---|---|
0001 |
“0,0,0 1,2,3 4,5,6” |
- 3) Extra_Cell_ROI_ID boundaries
##ROI_boundaries_format=Extra-cell ROI boundaries are reported in global coordinates using the OBJ format for 3D MESH models. As such boundaries are defined as lists of geometric vertices, with (x, y, z, [w]) coordinates, w is optional and defaults to 1.0.
|
|
|---|---|
0001 |
“v 0.123 0.234 0.345 1.0” |
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
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.
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_mapping |
|
##Cell_Type= |
This field records the type of extracellular structure ROIs used in this table represent. The value utilized should belong to this list: Primary cell line, Immortal cell line, Induced pluripotent stem (IPS) cell, Cell in tissue, Cell in organoid, |
Cell in tissue |
Conditional requirement: this MUST be reported in any Cell is idenfied as part of this experiment. |
##Sub_Cell_ROI_Type= |
This field records the type of extracellular structure ROIs used in this table represent. The value utilized should belong to this list: Nucleolus, NL, PML_body, Cajal_body, Chromosome_Domain, Other |
Nucleolus |
Conditional requirement: this MUST be reported in any Sub_Cell ROI is idenfied as part of this experiment. |
##Extra_Cell_ROI_Type= |
This field records the type of extracellular structure ROIs used in this table represent. The value utilized should belong to this list: Tissue, Organoid, Other |
Tissue |
Conditional requirement: this MUST be reported in any Super_Cell ROI is idenfied as part of this experiment. |
##ROI_Boundaries_Format= |
This field MUST be used to describe the format that is used to record the boundaries of the ROI in global coordinates. An option is the use of the OME ROI data model. Alternatively, 3D MESH models (e.g., using the OBJ format) can also be used. Additional formats are also allowed. |
(X1,Y1, X2,Y2 … Xn,Yn) |
|
##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 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. |
Mean Fluorescence 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. |
(Cell_ID, ROI_Boundaries, 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 Cell_ID, Sub_Cell_ROI_ID, or Extra_Cell_ROI_ID.
The first column of this table is always the relevant ID. The content and order of all other columns is at user’s discretion. The order of the rows is at user’s discretion.
It is mandatory to choose one of the three types of ID.
Name |
Description |
Example |
Conditional requirement conditions |
|---|---|---|---|
Sub_Cell_ROI_ID |
This fields reports the unique identifier for a Region of Interest (ROI) that represents the boundaries of a sub-cellular structure identified as part of this experiment. Note: this is used to connect all Spots, and Traces that belong to the same ROI. |
1 |
Conditional requirement: This table must have at least one of the ID columns. Sub_Cell_ROI_ID MUST be reported if this table contains subcellular ROI data |
Cell_ID |
This fields reports the unique identifier for Region of Interest (ROI) that represent the boundaries of a Cell identified as part of this experiment. Note: this is used to connect individual Spots or Traces that are part of the same Cell. |
1 |
Conditional requirement: This table must have at least one of the ID columns. Cell_ID MUST be reported if this table contains Cell data |
Extra_Cell_ROI_ID |
This fields reports the unique identifier for a Region of Interest (ROI) that represents the boundaries of a extracellular structure (e.g., Tissue) identified as part of this experiment. Note: this is used to connect all Spots, and Traces that belong to the same ROI. |
1 |
Conditional requirement: This table must have at least one of the ID columns. Extra_Cell_ROI_ID MUST be reported if this table contains extracellular ROI data. |
ROI_Boundaries |
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Optional_Column_1 |
|||
Optional_Column_2 |
|||
Optional_Column_3 |
Example
##FOF-CT_Version=v1.0
##Table_Namespace=4dn_FOF-CT_mapping
##Sub_Cell_ROI_Type=PML_body
##ROI_Boundaries_Format=(X1,Y1 X2,Y2 ... Xn,Yn)
##XYZ_Unit=micron
#Lab_Name: Nobel
#Experimenter_Name: John Doe
#Experimenter_Contact: john.doe@email.com
#Description: This table reports the boundaries of PML_bodies identified as part of this experiment and identified utilizing PML antibodies.
#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
#Additional_Tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace
##Columns=(Sub_Cell_ROI_ID, ROI_Boundaries)
1, (0,0 1,2 3,5)
2, (0,0 2,3 4,6)
3, (0,0 3,2 7,5)
4, (0,0 9,2 9,5)