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Extract_Images

Component
Description

A utility macro for the specified use of BioFormats plugin. Takes a folder of proprietary images formats (Zeiss zvi, lsm, czi or Nikon nd2) and extracts them to .tif images

The extracted images are located in a folder defined in the menu. Other options: reset spatial scales, reads ROIs, split channels, add stage position in the name.

<!-- [previous text] This macro allows to batch convert .zvi multichannel time-lapse movies into .tif stacks. There are several options for processing and filtering. In particular, you can register the jitter due to small stage movements during acquisition. For this option to work you need to install Kang Li's Image Stabilizer plugin. -->

note: The old name of the macro was "ZVI Extractor" and the data format was limited to ZVI, but the upgraded version includes more formats.

Requires Bio-Formats plugin

LIF Projector

Component
Description

This macro is similar to the LIF_Extractor, but it will output Z-projection of each Z-stack. You can choose the type of projection in addition to the other options. Requires Bio-Formats plugin

has function
Image projection

3View import list

Component
Description

The purpose of this plugin is to create a text file with a list of files from Gatan’s 3View montage image stacks. This text file can then be used to automatically import all the images into TrakEM2, as they are, stored in the original directories.

has topic
Serial block-face scanning electron microscopy
has function
Object tracking
Data handling
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