Zeiss LSM 880, Operating Manual

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CHAPTER 1 - SYSTEM OPERATION
LSM 880 Left Tool Area and Hardware Control Tools ZEISS
10/2014 V_01 000000-2071-464 381
5.4.19.3 Online Multiview Processing
Processing of a multiview experiment dataset can be done online during data acquisition while the data is
streamed onto a storage and analysis PC. ZEN software must be started on the storage and analysis PC
and the master file (*.czi) of the experiment can be opened.
It is possible to save dimensions of the experiment
as individual files. To do so, the dimensions can be
chosen with the according check box in the
Streaming tool window (Fig. 535) of the
Maintain tab
(see as well section
Maintain Tab
).
It is important that only the Time
checkbox is activated for
Online
Multiview Processing , which is the
default setting. If other dimensions are
separated (e.g. channels) they are not
included in the processing procedure and
will be missing in the resulting file.
When time series are acquired with the Lightsheet Z.1, the first time point is a master file with the
following appearance: Name.czi (e.g. FishEmbryogenesis.czi). For each time point, a separate file is
additionally formed in the same folder with the nomenclature: Name(time point-1).czi (e.g.
FishEmbryogensis(221).czi). This master file must be selected in the
Method Parameters window. There,
the settings for processing can be chosen as described in the section Multiview Processing .
When pressing the Apply button, processing will start for the already acquired images of the time series.
The registration option:
Interactive registration
is not available for
Online Multiview Processing
and
is missing from the according drop down menu. To use this registration during the acquisition of the time
series, please proceed as following. Open one time point of the experiment and choose the
Multiview
Processing
option and press the
Select
button. Follow the description in section
Multiview Processing
to perform an interactive registration. When pressing the Apply button, an .xml file is created in the
Result folder, which holds all registration information. The Result folder is created within the folder of
the original dataset.
Proceed by opening the master file (first time point) of the ongoing experiment and choose
Online
Multiview Processing . Press the Select button and choose Registration from file from the drop down
menu. Follow the instructions in section
Multiview Processing
.
Fig. 535 Streaming tool window