pyHiM chromatin trace format#
This page describes the format of pyHiM chromatin trace tables.
Summary#
The chromatin trace table is the main output of pyHiM and records the primary results. The table contains the 3D coordinates of single DNA-FISH spots that are spatially linked together in single 3D chromatin traces.
Tables have to have 12 columns:
{name: Spot_ID, datatype: string}
{name: Trace_ID, datatype: string}
{name: x, datatype: float32}
{name: y, datatype: float32}
{name: z, datatype: float32}
{name: Chrom, datatype: string}
{name: Chrom_Start, datatype: int64}
{name: Chrom_End, datatype: int64}
{name: ‘ROI #’, datatype: int64}
{name: Mask_id, datatype: int64}
{name: ‘Barcode #’, datatype: int64}
{name: label, datatype: string}
Spot_ID contains a unique identifier for a spot. Spots with the same Trace_ID, by definition, belong to the same chromatin trace. xyz coordinates are provided in $\um$ (microns) units. Chrom describes the identity of the chromosome being targeted, with Chrom_Start and Chrom_End containing the genomic coordinates in basepairs. ROI # describes the Region of Interest where the trace was acquired, Mask_id describes the identity of the mask to which the trace was associated with, Barcode # indicates the identity of the barcode, and label the name of the region or cell type associated with the trace.
In this table the reported x, y, z coordinates are assumed to result from post-processing and quality control procedures and therefore correspond to the final localization of the DNA target under study.
Trace table have extension ecsv and are written and read by astropy or by pandas.
Example#
The following contains the first rows of a typical chromatin trace table.
# %ECSV 1.0
# ---
# datatype:
# - {name: Spot_ID, datatype: string}
# - {name: Trace_ID, datatype: string}
# - {name: x, datatype: float32}
# - {name: y, datatype: float32}
# - {name: z, datatype: float32}
# - {name: Chrom, datatype: string}
# - {name: Chrom_Start, datatype: int64}
# - {name: Chrom_End, datatype: int64}
# - {name: 'ROI #', datatype: int64}
# - {name: Mask_id, datatype: int64}
# - {name: 'Barcode #', datatype: int64}
# - {name: label, datatype: string}
# schema: astropy-2.0
Spot_ID Trace_ID x y z Chrom Chrom_Start Chrom_End "ROI #" Mask_id "Barcode #" label
c001209e-0a70-4d72-b0d9-1541747a48bb 9d75fd7d-b170-4703-bd2c-810e77757990 100.532814 10.439153 10.996869 xxxxx 0 999999999 17 12 3 OK107
ae281ab3-1c01-4e1b-8dff-c6fa7242548b 9d75fd7d-b170-4703-bd2c-810e77757990 100.79655 10.506308 11.150922 xxxxx 0 999999999 17 12 12 OK107
3eafffb3-0d84-4528-b689-3babbe7e6f25 9d75fd7d-b170-4703-bd2c-810e77757990 100.55611 10.479042 11.213325 xxxxx 0 999999999 17 12 10 OK107
59a53a22-9f97-4253-a2b7-85c7bf388d5f 9d75fd7d-b170-4703-bd2c-810e77757990 100.588234 10.45398 11.16187 xxxxx 0 999999999 17 12 708 OK107
eeb8eaff-cb9a-4b6d-be7c-dd1fdf7ed903 9d75fd7d-b170-4703-bd2c-810e77757990 100.54249 10.473159 11.117058 xxxxx 0 999999999 17 12 8 OK107
f5898628-5dc9-475f-ae8a-50a585442c7b 9d75fd7d-b170-4703-bd2c-810e77757990 100.62601 10.43174 11.196201 xxxxx 0 999999999 17 12 639 OK107
c69259b8-fe30-461f-b254-948b0fb39eee 9d75fd7d-b170-4703-bd2c-810e77757990 100.50262 10.438758 11.308915 xxxxx 0 999999999 17 12 11 OK107
a706a795-3b16-47d8-a79c-6ca89645b5a8 9d75fd7d-b170-4703-bd2c-810e77757990 100.492516 10.462756 11.23178 xxxxx 0 999999999 17 12 9 OK107
2e2ba97a-c56c-42d5-87a7-38d1a44850a5 f869e519-4055-4b33-a908-baf2b832db2f 86.96675 166.51755 9.938585 xxxxx 0 999999999 17 17 17 OK107
1ec18364-f716-4cd0-aa5c-d8a31d99ce83 f869e519-4055-4b33-a908-baf2b832db2f 86.920494 166.58627 9.994431 xxxxx 0 999999999 17 17 16 OK107
49934fc9-be19-4720-97b8-aef2ee64b904 2b53ea53-b85d-4012-a391-df4db9af3e4b 107.340935 68.58549 9.746644 xxxxx 0 999999999 17 36 20 OK107
d0756e97-8ebc-4e6d-9826-e868f52fc01b 2b53ea53-b85d-4012-a391-df4db9af3e4b 107.22091 68.564255 9.5504875 xxxxx 0 999999999 17 36 708 OK107
d106fc7a-2ba1-4ff1-8064-07604616b5f1 2b53ea53-b85d-4012-a391-df4db9af3e4b 107.28838 68.52376 9.712829 xxxxx 0 999999999 17 36 21 OK107