MRI_Opera_export_tools

The tool stitches images from the Opera Phenix HCS System. It reads the Index.idx.xml file to pre-arrange the images and then stitches and fuses them using the Grid/Collection stitching-plugin. Images are stitched by plane and channel. Z-stacks and multi-channel images can optionally be created. Projections can also be created.

The source code in git-hub can be found here.

Getting started

To install the tool save the files opera_export_tools.ijm and opera_export_tools.py into the folder macros/toolsets of your FIJI installation.

Select the "opera_export_tools" toolset from the >> button of the ImageJ launcher.

• the first button opens this help page
• second button allows to select the index-file
• the third button allows to select the wells, that will be exported
• the fourth button allows to modify the export options
• the fifth button starts the batch-export

Usage

Step 1 - Select the index-file

Press the Set index-file-button and navigate to the folder containing the images. Select the index file Index.idx.xml.

Step 2 - Select the wells

Press the Select wells-button and select the wells you want to export. If export all is selected, all wells will be exported.

Step 3 - Modify the export-options

Press Set options-button.

z-slice for stitching

The z-slice, that is used to calculate the stitching. Enter 0 to use the middle slice.

channel for stitching

The channel, that is used to calculate the stitching

create z-stack

If selected one file per z-stack is created, otherwise one per slice is created.

merge channels

If selected the channels are merged into a hyperstack-image.

apply z-projection

If selected a maximum intensity projection (mip) is created instead of a z-stack.

pseudo flat field radius

The radius for the pseudo flat field correction. Set the radius to 0 if you do not want to apply a pseudo flat field correction. You must have the biovoxxel toolbox installed

rolling ball radius

The radius for the rolling-ball background correction. Set the radius to 0 if you do not want to apply a rolling-ball background correction.

normalize

If selected the the intensities of the tiles of a mosaic are normalized.

find background radius

The radius for the find and subtract background operation. Set the radius to 0 if you do not want to apply the find and subtract background operation.

Fusion parameters:

The parameters for the stitching plugin

Colours

Set the colours of the first seven channels.

Results

The result images will be written into a subfolder out of the folder that contains the index-file.