ImageJ plugin: BF Exporter not saving applied settings

[dgault]

This has been reported by a number of users, often who are applying LUT or in the case of https://forum.image.sc/t/saving-a-mask-with-bio-formats/34905 a threshold is applied to the image to create a mask.

Any of the ImageJ settings applied after import are not included in the saved file when exporting again.

To reproduce:

• Import an image to ImageJ using the Bio-Formats Importer
• Apply any settings from the Image drop down
• Use the Bio-Formats Exporter to save the image
• Re import the image and the settings which had been applied will not have been saved

I had thought there was an existing issue for this but was not able to find it, if this is a duplicate please link to the original issue and I will merge the 2.

[dgault]

A further report of this issue has been made on imagesc thread: https://forum.image.sc/t/bio-formats-does-not-recognize-setmetadata-info-string-or-property-setlist-string-image-info/46894

An additional issue with the plugin is that the Exporter is automatically concatenating images when an existing filename is used. The command line tools give the user the option to overwrite the existing file. This overwrite behaviour should be replicated in the Exporter plugin as well.