merging changes from #35

4dn-dcic · Aug 28, 2024 · 3f2b3c6 · 3f2b3c6
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diff --git a/docs/source/bio.rst b/docs/source/bio.rst
@@ -24,8 +24,8 @@ This table is mandatorily indexed by Spot_ID.
 File Header
 -----------
 - For full instructions see :ref:`headers-reference-label`
-- 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``.
+- 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``.
 
 The header **MUST** contain a mandatory set of fields that describe any algorithm that was used to produce/process data in this table. In case more than one algorithm were used, please use the same set of fields for each of them.
 

diff --git a/docs/source/cell.rst b/docs/source/cell.rst
@@ -19,8 +19,8 @@ table with data stored in one of the other tables (e.g.,
 File Header
 -----------
 - For full instructions see :ref:`headers-reference-label`
-- 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``.
+- 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``.
 
 The header **MUST** include a detailed description of each optional columns used.
 

diff --git a/docs/source/core.rst b/docs/source/core.rst
@@ -46,8 +46,8 @@ Instructions for reporting the location of DNA Spots and Traces in case the geno
 File Header
 -----------
 - For full instructions see :ref:`headers-reference-label`
-- 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``.
+- 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``.
 
 The header **MUST** contain a mandatory set of fields that describe the
 algorithm(s) that were used to identify and localize bright Spots and to

diff --git a/docs/source/demultiplexing.rst b/docs/source/demultiplexing.rst
@@ -20,8 +20,8 @@ Other columns are at user's discretion.
 File Header
 -----------
 - For full instructions see :ref:`headers-reference-label`
-- 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``.
+- 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``.
 
 The header **MUST** contain a mandatory set of fields that describe any
 algorithm that was used to produce/process data in this table.

diff --git a/docs/source/examples/bio b/docs/source/examples/bio
@@ -1,20 +1,20 @@
-##FOF-CT_version=v1.0
-##Table_namespace=4dn_FOF-CT_bio
-##XYZ_unit=micron
-#lab_name: Nobel
-#experimenter_name: John Doe
-#experimenter_contact: john.doe@email.com
-#description: In this experiment cells were identified by segmentation using the indicated algorithm on the basis of the background fluorescence from multiplexed FISH probes.
+##FOF-CT_Version=v1.0
+##Table_Namespace=4dn_FOF-CT_bio
+##XYZ_Unit=micron
+#Lab_Name: Nobel
+#Experimenter_Name: John Doe
+#Experimenter_Contact: john.doe@email.com
+#Description: In this experiment cells were identified by segmentation using the indicated algorithm on the basis of the background fluorescence from multiplexed FISH probes.
 #Software_Title: AlgorithmXYZ
 #Software_Type: Distance
 #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
-#^NL_distance: the Euclidean 3D distance between the centroid of the indicated DNA Spot and the Nuclear Lamina identified using the convex hull surrounding all detected chromatin loci, as described in Doe et al., 20221.
-#^H4K27me3_distance: the Euclidean 3D distance between the centroids of the indicated DNA Spot and the closest H4K27me3 signal, respectively. H4K27me3 enriched chromatin was detected using the XYZ antibody as described in Doe et al, 2021.
-#additional_tables: 4dn_FOF-CT_rna, 4dn_FOF-CT_cell
-##columns=(Spot_ID, NL_distance, H4K27me3_distance)
+#^NL_Distance: the Euclidean 3D distance between the centroid of the indicated DNA Spot and the Nuclear Lamina identified using the convex hull surrounding all detected chromatin loci, as described in Doe et al., 20221.
+#^H4K27me3_Distance: the Euclidean 3D distance between the centroids of the indicated DNA Spot and the closest H4K27me3 signal, respectively. H4K27me3 enriched chromatin was detected using the XYZ antibody as described in Doe et al, 2021.
+#Additional_Tables: 4dn_FOF-CT_rna, 4dn_FOF-CT_cell
+##Columns=(Spot_ID, NL_Distance, H4K27me3_Distance)
 1, 1.345, 0.445
 2, 1.245, 0.005
 3, 1.005, 0.150
diff --git a/docs/source/examples/cell b/docs/source/examples/cell
@@ -1,12 +1,12 @@
-##FOF-CT_version=v1.0
-##Table_namespace=4dn_FOF-CT_cell
-##Cell_type=Cell in organoid
+##FOF-CT_Version=v1.0
+##Table_Namespace=4dn_FOF-CT_cell
+##Cell_Type=Cell in organoid
 ##Extra_Cell_ROI_type=Organoid
-##XYZ_unit=micron
-#lab_name: Nobel
-#experimenter_name: John Doe
-#experimenter_contact: john.doe@email.com
-#description: In this experiment cells were identified by segmentation using the indicated algorithm on the basis of the background fluorescence from multiplexed FISH probes.
+##XYZ_Unit=micron
+#Lab_Name: Nobel
+#Experimenter_Name: John Doe
+#Experimenter_Contact: john.doe@email.com
+#Description: In this experiment cells were identified by segmentation using the indicated algorithm on the basis of the background fluorescence from multiplexed FISH probes.
 #Software_Title: AlgorithmXYZ
 #Software_Type: Segmentation
 #Software_Authors: John Doe
@@ -15,10 +15,10 @@
 #Software_PreferredCitationID: https://doi.org/doi_goes_here
 #^RNA_A_nr: the number of detected bright Spots corresponding to RNA transcript A detected in this Cell, see also RNA Spot Data table
 #^RNA_B_nr: the number of detected bright Spots corresponding to RNA transcript B detected in this Cell, see also RNA Spot Data table
-#^cell_cycle_state: the Cell Cycle state in which this Cell is found as measured with the Fucci system. This column can contain one of the following values: G1, S, G2 or M.
-#^cell_volume: the volume of this Cell expressed in micron^3.
-#additional_tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace
-##columns=(Cell_ID, Extra_Cell_ROI_ID, RNA_A_nr, RNA_B_nr, cell_cycle_state, cell_volume)
+#^Cell_Cycle_State: the Cell Cycle state in which this Cell is found as measured with the Fucci system. This column can contain one of the following values: G1, S, G2 or M.
+#^Cell_Volume: the volume of this Cell expressed in micron^3.
+#Additional_Tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace
+##Columns=(Cell_ID, Extra_Cell_ROI_ID, RNA_A_nr, RNA_B_nr, Cell_Cycle_State, Cell_Volume)
 1, 1, 10, 22, 1041.5, 12354.24, G1, 13453
 2, 1, 0, 11, 2041.3, 32234.24, G2, 35545
 3, 2, 10, 33, 101.5, 12354.24, S, 10010

diff --git a/docs/source/examples/core b/docs/source/examples/core
@@ -1,19 +1,19 @@
-##FOF-CT_version=v1.0
-##Table_namespace=4dn_FOF-CT_core
-##genome_assembly=GRCh38
-##XYZ_unit=micron
-#lab_name: Nobel
-#experimenter_name: John Doe
-#experimenter_contact: john.doe@email.com
-#description: Lorem ipsum dolor sit amet, consectetur adipiscing elit. Maecenas sagittis est mollis, pulvinar tortor mattis, dignissim nisi. Nunc tincidunt volutpat lacus vitae bibendum.
+##FOF-CT_Version=v1.0
+##Table_Namespace=4dn_FOF-CT_core
+##Genome_Assembly=GRCh38
+##XYZ_Unit=micron
+#Lab_Name: Nobel
+#Experimenter_Name: John Doe
+#Experimenter_Contact: john.doe@email.com
+#Description: Lorem ipsum dolor sit amet, consectetur adipiscing elit. Maecenas sagittis est mollis, pulvinar tortor mattis, dignissim nisi. Nunc tincidunt volutpat lacus vitae bibendum.
 #Software_Title: ChrTracer3
 #Software_Type: SpotLoc+Tracing
 #Software_Authors: Mateo, LJ; Sinnott-Armstrong, N; Boettiger, AN
 #Software_Description: ChrTracer3 software was developed for analysis of raw DNA labeled images. As an input, it takes an.xlsx table containing information and folder names of the DNA experiment. As an output, it returns tab delimited.txt ﬁles with drift-corrected x, y, z positions for all labeled barcodes. These can be used directly to calculate the nm scale distances between all pairs of labeled loci. The current version of the software as of this writing is ChrTracer3.
 #Software_Repository: https://github.com/BoettigerLab/ORCA-public
 #Software_PreferredCitationID: https://doi.org/10.1038/s41596-020-00478-x
-#additional_tables: 4dn_FOF-CT_quality, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell
-##columns=(Spot_ID, Trace_ID, X, Y, Z, Chrom, Chrom_Start, Chrom_End, Cell_ID)
+#Additional_Tables: 4dn_FOF-CT_quality, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell
+##Columns=(Spot_ID, Trace_ID, X, Y, Z, Chrom, Chrom_Start, Chrom_End, Cell_ID)
 1, 1, 14.43, 41.43, 1.23, chr1, 0001, 1000, 1
 2, 1, 14.83, 41.83, 1.83, chr1, 1001, 2000, 1
 3, 1, 15.83, 42.83, 1.33, chr1, 2001, 3000, 1

diff --git a/docs/source/examples/demultiplexing b/docs/source/examples/demultiplexing
@@ -1,23 +1,23 @@
-##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
+##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
+#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)
+#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

diff --git a/docs/source/examples/extracell b/docs/source/examples/extracell
@@ -1,11 +1,11 @@
-##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
-#experimenter_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.
+##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
@@ -14,9 +14,9 @@
 #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)
+#^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

diff --git a/docs/source/examples/mapping b/docs/source/examples/mapping
@@ -1,20 +1,20 @@
-##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.
+##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)
+#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)

diff --git a/docs/source/examples/quality b/docs/source/examples/quality
@@ -1,11 +1,11 @@
-##FOF-CT_version=v1.0
-##Table_namespace=4dn_FOF-CT_quality
-##XYZ_unit=micron
-##intensity_unit=photonCount
-#lab_name: Nobel
-#experimenter_name: John Doe
-#experimenter_contact: john.doe@email.com
-#description:  Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
+##FOF-CT_Version=v1.0
+##Table_Namespace=4dn_FOF-CT_quality
+##XYZ_Unit=micron
+##Intensity_Unit=photonCount
+#Lab_Name: Nobel
+#Experimenter_Name: John Doe
+#Experimenter_Contact: john.doe@email.com
+#Description:  Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
 #Software_Title: SpotQualityCheck
 #Software_Type: QualityControl
 #Software_Authors: John Doe et al.
@@ -26,8 +26,8 @@
 #^X_Loc_Precision: lower and upper bound of 95% confidence interval on X-position after fit
 #^Y_Loc_Precision: lower and upper bound of 95% confidence interval on Y-position after fit
 #^Z_Loc_Precision: lower and upper bound of 95% confidence interval on Z-position after fit
-#additional_tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell
-##columns=(Spot_ID, Channel_Name, Fluorophore_Name, Peak_Intensity, Raw_X, Raw_Y, Raw_Z, X_Drift, Y_Drift, Z_Drift, X_Chromatic_Shift, Y_Chromatic_Shift, Z_Chromatic_Shift, X_Loc_Precision, Y_Loc_Precision, Z_Loc_Precision)
+#Additional_Tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell
+##Columns=(Spot_ID, Channel_Name, Fluorophore_Name, Peak_Intensity, Raw_X, Raw_Y, Raw_Z, X_Drift, Y_Drift, Z_Drift, X_Chromatic_Shift, Y_Chromatic_Shift, Z_Chromatic_Shift, X_Loc_Precision, Y_Loc_Precision, Z_Loc_Precision)
 001, 510/25, AlexaFluor_488, 1.1, 1.05, 1.2, 0.1, 0.05, 0.2, 0.2, 0.2, 0.2, 0.01, 0.01, 0.01
 002, 510/25, AlexaFluor_488, 1.11, 1.055, 1.22, 0.11, 0.055, 0.22, 0.22, 0.22, 0.22, 0.012, 0.012, 0.012
 003, 510/25, AlexaFluor_488, 1.12, 1.054, 1.21, 0.12, 0.054, 0.21, 0.22, 0.22, 0.22, 0.012, 0.012, 0.012

diff --git a/docs/source/examples/rna b/docs/source/examples/rna
@@ -1,20 +1,20 @@
-##FOF-CT_version=v1.0
-##Table_namespace=4dn_FOF-CT_rna
-##genome_assembly=GRCh38
-##XYZ_unit=micron
+##FOF-CT_Version=v1.0
+##Table_Namespace=4dn_FOF-CT_rna
+##Genome_Assembly=GRCh38
+##XYZ_Unit=micron
 ##Gene_ID_type=Ensemble_V38
-#lab_name: Nobel
-#experimenter_name: John Doe
-#experimenter_contact: john.doe@email.com
-#description: Lorem ipsum dolor sit amet, consectetur adipiscing elit. Maecenas sagittis est mollis, pulvinar tortor mattis, dignissim nisi. Nunc tincidunt volutpat lacus vitae bibendum.
+#Lab_Name: Nobel
+#Experimenter_Name: John Doe
+#Experimenter_Contact: john.doe@email.com
+#Description: Lorem ipsum dolor sit amet, consectetur adipiscing elit. Maecenas sagittis est mollis, pulvinar tortor mattis, dignissim nisi. Nunc tincidunt volutpat lacus vitae bibendum.
 #Software_Title: Xyz
 #Software_Type: SpotLoc
 #Software_Authors: Janet Doette
 #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_quality, 4dn_FOF-CT_cell
-##columns=(Spot_ID, X, Y, Z, RNA_name, Gene_ID, Transcript_ID, Trace_ID)
+#Additional_Tables: 4dn_FOF-CT_core, 4dn_FOF-CT_quality, 4dn_FOF-CT_cell
+##Columns=(Spot_ID, X, Y, Z, RNA_name, Gene_ID, Transcript_ID, Trace_ID)
 001, 14.43, 41.43, 1.23, ACTB, ENSG00000075624, ENST00000646664.1, 001
 002, 14.83, 41.83, 1.83, GAPDH, ENSG00000111640, ENST00000229239.10, 001
 003, 15.83, 42.83, 1.33, MB, ENSG00000198125, ENST00000397326.7, 001
diff --git a/docs/source/examples/rna_bio b/docs/source/examples/rna_bio
@@ -1,10 +1,10 @@
-##FOF-CT_version=v1.0
-##Table_namespace=4dn_FOF-CT_rna_bio
-##XYZ_unit=micron
-#^NL_distance: the Euclidean 3D distance between the centroid of the indicated RNA Spot and the Nuclear Lamina identified using the convex hull surrounding all detected chromatin loci, as described in Doe et al., 20221.
-#^H4K27me3_distance: the Euclidean 3D distance between the centroids of the indicated RNA Spot and the closest H4K27me3 signal, respectively. H4K27me3 enriched chromatin was detected using the XYZ antibody as described in Doe et al, 2021.
-#additional_tables: 4dn_FOF-CT_rna, 4dn_FOF-CT_cell
-##columns=(RNA_Spot_ID, NL_distance, H4K27me3_distance)
+##FOF-CT_Version=v1.0
+##Table_Namespace=4dn_FOF-CT_rna_bio
+##XYZ_Unit=micron
+#^NL_Distance: the Euclidean 3D distance between the centroid of the indicated RNA Spot and the Nuclear Lamina identified using the convex hull surrounding all detected chromatin loci, as described in Doe et al., 20221.
+#^H4K27me3_Distance: the Euclidean 3D distance between the centroids of the indicated RNA Spot and the closest H4K27me3 signal, respectively. H4K27me3 enriched chromatin was detected using the XYZ antibody as described in Doe et al, 2021.
+#Additional_Tables: 4dn_FOF-CT_rna, 4dn_FOF-CT_cell
+##Columns=(RNA_Spot_ID, NL_Distance, H4K27me3_Distance)
 1, 1.345, 0.445
 2, 1.245, 0.005
 3, 1.005, 0.150
diff --git a/docs/source/examples/rna_quality b/docs/source/examples/rna_quality
@@ -1,11 +1,11 @@
-##FOF-CT_version=v1.0
-##Table_namespace=4dn_FOF-CT_rna_quality
-##XYZ_unit=micron
-##intensity_unit=photonCount
-#lab_name: Nobel
-#experimenter_name: John Doe
-#experimenter_contact: john.doe@email.com
-#description:  Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
+##FOF-CT_Version=v1.0
+##Table_Namespace=4dn_FOF-CT_rna_quality
+##XYZ_Unit=micron
+##Intensity_Unit=photonCount
+#Lab_Name: Nobel
+#Experimenter_Name: John Doe
+#Experimenter_Contact: john.doe@email.com
+#Description:  Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
 #Software_Title: SpotQualityCheck
 #Software_Type: QualityControl
 #Software_Authors: John Doe et al.
@@ -26,8 +26,8 @@
 #^X_Loc_Precision: lower and upper bound of 95% confidence interval on X-position after fit
 #^Y_Loc_Precision: lower and upper bound of 95% confidence interval on Y-position after fit
 #^Z_Loc_Precision: lower and upper bound of 95% confidence interval on Z-position after fit
-#additional_tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell
-##columns=(RNA_Spot_ID, Channel_Name, Fluorophore_Name, Peak_Intensity, Raw_X, Raw_Y, Raw_Z, X_Drift, Y_Drift, Z_Drift, X_Chromatic_Shift, Y_Chromatic_Shift, Z_Chromatic_Shift, X_Loc_Precision, Y_Loc_Precision, Z_Loc_Precision)
+#Additional_Tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell
+##Columns=(RNA_Spot_ID, Channel_Name, Fluorophore_Name, Peak_Intensity, Raw_X, Raw_Y, Raw_Z, X_Drift, Y_Drift, Z_Drift, X_Chromatic_Shift, Y_Chromatic_Shift, Z_Chromatic_Shift, X_Loc_Precision, Y_Loc_Precision, Z_Loc_Precision)
 001, 510/25, AlexaFluor_488, 1.1, 1.05, 1.2, 0.1, 0.05, 0.2, 0.2, 0.2, 0.2, 0.01, 0.01, 0.01
 002, 510/25, AlexaFluor_488, 1.11, 1.055, 1.22, 0.11, 0.055, 0.22, 0.22, 0.22, 0.22, 0.012, 0.012, 0.012
 003, 510/25, AlexaFluor_488, 1.12, 1.054, 1.21, 0.12, 0.054, 0.21, 0.22, 0.22, 0.22, 0.012, 0.012, 0.012