PYMEImage (dh5view) - Image Data Analysis and Viewing

DSView is a general purpose data viewer that supports all the PYME Data Formats and additionally the QUEUE objects used in real-time data analysis. DSView may either be invoked with the command:

dh5view [options] filename

or launched programatically by passing a numpy array or PYME datasource to PYME.DSView.View3D(...).

Modules

DSView has a number of modules for performing various analysis tasks, including Localisation Analysis, PSF Extraction, Deconvolution, and Tiling.

Modes

Modes represent personalities suitable for use with certain types of data and determine which modules are loaded on startup. The mode used is determined by filename, although modules which are not loaded by default can be inserted later from the Modules menu.

The modes are:

Name

File types

Description

lite

programatic invocation

no modules loaded

LM

.h5, QUEUE

localisation analysis

blob

.tif

blob analysis and PSF extraction

default

aything else

PSF extraction

A particular mode can be forced by calling dh5view with the -m option, eg:

dh5view -m LM filename