FCS文件标准升级：从2.0到3.2，流式细胞数据分析新时代
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更新于2024-08-03
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流式细胞文件 (FCS) 标准协议是1990年由Wiley-Liss, Inc.发布的一个关键的标准化文件，旨在为流式细胞术数据提供详尽的描述和交换机制。该协议在当时是行业的基石，用于确保不同实验室之间的流式细胞仪数据能够准确、一致地共享。然而，随着技术的进步，原始的FCS 1.0/2.0版本已经显得过时，现在的最新版本已发展至3.2，这体现了技术更新和标准演进的重要性。
FCS 2.0版标准定义了一个数据文件结构，其主要组成部分包括：
1. **HEADER**：这是文件的元数据部分，包含了关于数据集的重要信息，如使用的仪器型号、样本描述、采集日期等。这部分非常重要，因为它是解析文件的关键，且始终位于文件的开头。
2. **TEXT**：这一部分可包含实验者注释、方法描述、样本处理步骤等非数值数据，有助于理解数据的上下文和实验条件。
3. **DATA**：这是核心部分，存储了实际的测量数据，包括各通道的荧光强度或其他流式参数，通常以二进制形式表示，记录了单个或多个样本的每次采集的数据点。
4. **ANALYSIS**：这部分可能包含对原始数据的初步分析结果，如直方图、聚类分析或其他计算结果，有助于科学家快速了解数据分析的初步见解。
FCS 2.0文件设计为连续的字节流，没有行或页格式，使得文件可以在不同的系统和平台之间无缝传输，即使硬件或软件发生变化也能保持兼容性。然而，随着科技的发展，新版本的FCS标准在数据压缩、文件加密、元数据扩展等方面进行了优化，以适应现代技术的需求和数据安全考虑。
尽管FCS 2.0标准在早期的流式细胞术研究中扮演了重要角色，但推荐使用更新的版本（如3.2）以确保数据的完整性和准确性，同时享受最新的功能和性能提升。对于科研人员来说，熟悉并遵循这些标准至关重要，因为它不仅影响数据的质量，还影响着整个科学社区的研究成果可重复性和透明度。
0
1990
Wiley-Liss,
Inc.
Cytometry
11:323-332
(1990)
Data
File
Standard for
Flow
Cytometry
Data File Standards Committee
of
the Society
for
Analytical Cytology
Received for publication November
27,
1989; accepted November
27,
1989
This data file standard for flow cytom-
etry (FCS) provides a detailed descrip-
tion of
a
data file structure designed such
that the file can include all of the infor-
mation necessary to describe fully:
1)
the
instrument used to obtain the data; 2) the
sample measured;
3)
the data obtained;
and
4)
the results of analysis of the data.
The file may contain one
or
more data
sets. Each data set includes data from
a
single sample
or
acquisition run. Each
data set consists of
a
minimum of four
parts-HEADER, TEXT, DATA, and
ANALYSIS-all of which are required.
The file is structured such that the parts
of
a
data set do not have to be in any par-
ticular order, except for the HEADER,
which must always be first. The
HEADER contains pointers to the begin-
ning and end of each of the other three
parts. The file is written
as
a
continuous
byte stream, with no line or page format-
ting. The HEADER, TEXT, and ANALY-
SIS parts are written in ASCII format
and the DATA part can be written in
ASCII, binary integer or floating point.
This Standard, noted as FCS2.0, is
based on
a
standard proposed by Mur-
phy and Chused
(Cytonetry
5:553-555,
1984).
Data
written utilizing their pro-
posed format (FCSl.0)
is
compatible with
the format described here. Future ver-
sions of the standard will maintain com-
patibility with older versions.
1.
2.
3.
4.
5.
6.
7.
GENERAL PRINCIPLES
A data set contains all of the information relative
to a flow cytometric measurement.
Data from more than one measurement may be
stored in
a
single file, as a number of data sets.
Each data
set
contains four mandatory parts
(HEADER, TEXT, DATA, and ANALYSIS) and
any number of additional (user-defined) parts.
Each data set
is
complete unto itself, not depen-
dent on any other data set in the data file.
The HEADER is always the first part of
a
data
set.
It
contains the byte address of the beginning
and end of all other parts of a data set, relative to
the beginning of the data set. This feature means
that the parts do not have to be contiguous or in a
particular order.
The TEXT part of a data set contains
KEY-
WORDS
and their associated
VALUES.
The form
of
a keyword value depends on the nature of the
keyword (e.g., character string or number). There
is
NO
default for any keyword. Keywords and
their values may be of any length (number of
bytes) except that they must contain at least one
character (no nulls). Keywords are case (upper/
lower) insensitive; values are case sensitive.
FCS keywords begin with the
“$”
character. They
are recognized by all programs with formats
as
specified in the Standard. User-defined keywords
must begin with some other character.
8. There are
required
and
optional
keywords. The
required keywords contain all of the information
necessary to read the data part of the data set.
Optional keywords are used to supply additional
information about the measurement.
9.
All space within
a
file which is not being used will
be filled with
a
space character.
SPECIFIC FILE PARTS
HEADER
The HEADER part of each data
set
in
a
data file
begins with the Flow Cytometry Standard version
identifier, which occupies the first 10 bytes. This ver-
sion of the Standard will be entered
as
“FCS2.0” fol-
lowed by four spaces. The next eight
(8)
bytes contain
the offset, in bytes, from the beginning of the data set
to the
start
of
the TEXT part of the data set; i.e., an
offset of 60 bytes points to the 61st byte of the data set.
All offsets are in ASCII, right justified. The next eight
(8)
bytes contain the offset, again in bytes, from the
beginning of the data set to the last byte of the TEXT
part. The next four
(4)
8-byte numbers give the offsets
to the beginning and end of the DATA part, and the
beginning and end of the ANALYSIS part. If any part
of the data set is not included in the file, the offsets can
be zero
(0)
or blank. Additional pairs of locally defined
offsets may follow the standard three
(3)
pairs if de-
sired. Thus, the
first
58 bytes of the data
set
are of fixed
format and contain information that identifies the ver-
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