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ImageJ plugin for handling NDPI files.

Home Page: http://www3.unifr.ch/bioimage/microscopes/slide-scanner/hamamatsu-nanozoomer-med/

Java 100.00%
imagej-plugins imagej imagej2 microscopy

nanozoomer-j's Introduction

NanoZoomer-J

NanoZoomer-J is a small collection of ImageJ plugins to deal with the NDPI image file format. The NDPI Converter > [...] OME-TIF Converter converter uses Bio-Formats to convert the proprietary file format to the ome.tif without loading the entire file into memory, which is important given that ndpi-files may be too big for the computer's memory.

Installation

The packaged binaries can be found on the release-page. To install the plugin in ImageJ, the downloaded jar-file can be dragged and dropped on the ImageJ main UI, or via the main menu: Plugins > Install PlugIn...

Usage

Once the jar has been added to ImageJ, the plugins can be run via the menu: Plugins > NDPI Converter > ...

Batch Converter

The batch converter takes an input directory, searches it for ndpi files and then lets you choose the channels and the pixel size for conversion. Once the directory has been selected, it takes a short moment to read the metadata from the first ndpi file. The order of the channels can be chosen by sequentially clicking on them in the selection table. All the channels are then merged into a single multichannel ome.tif.

Note: When converting a bright-field image, it treats the RGB as channels. So when opening the resulting ome.tif we get a color stack.

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