Home

Welcome to the Operetta Importer Wiki

This tool aims to simplify the export images from Operetta systems into something useable downstream.

Notable features

• Raw tiff files are loaded in parallel for each Field
• Specific Wells and Fields can be selected
• Specific channels, slices and frames can be selected
• XY data can be downsampled
• Z projection of data (Mean, Max, Sum, ...)
• Can use acquisition stage coordinates to fuse fields
• Can use Grid/Collection Stitching in order to align tiles and fuse fields

Getting started

Installation

This plugin is part of the PTBIOP update site. To make it available, please activate the PTBIOP update site in your Fiji installation.

Use (Interactive Tutorial)

Here are the parameters of the user interface and their uses

Parameter	Effect
Downsample factor	By how much to reduce the XY size of the original data. Useful when testing export settings
Use averaging when downsampling	If checked, the data will be smoothed before dowsampling, leading to a lower noise image
Save directory	Location where the exported images should be saved
Selected Wells	Optional using the "Choose Wells" button, you can specify a subset of wells to export. Useful while testing export parameters
Selected Fields	Optional using the "Choose Fields" button, you can specify a subset of Fields to export for each Well. Useful while testing export parameters
Fuse Fields	Options Do not fuse fields Each field will be exported individually Fuse using stage coordinates: Will place the fields of a given well into a single image, based on each field's position extracted from the metadata. No stitching is performed (fast) Fuse using 'Grid/Collection Stitching' plugin: Will stitch and fuse the fields using blending in the same way that the Grid/Collection Stitching plugin would
Flip images	This can be necessry depending on how your stage is set. If you notice that the fused fields do not match at the edges, test different settings. Do not flip: Exports the data as is Flip horizontal: Mirror the image data plane by plane horizontally. Flip vertical: Mirror the image data plane by plane verticalle. Flip both: Horizontal and vertical flipping
Select ranges	Allows to select sub-ranges for Channels, Slices and Frames. Use commas to separate single points or colons to define ranges (inclusive)
Perform projection	Can call the 'Z Projector' from ImageJ to project Z slices according to the available methods
Min Value	The minimum intensity value of the DPC image that will be set to 0 in the resulting stack
Max Value	The maximum intensity value of the DPC image that will be set to 65535
Processs	Clicking this button will save export the data to the designated folder with all the settings that were made in the user interface

Use (Scripting Tutorial)

How to's

Export contiguous Fields per Well

API reference (JavaDoc)