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Ticket Resolution Summary Owner Reporter
#226 fixed "Use virtual stack" option for Bio-Formats Importer melissa curtis

Reported by curtis, 12 years ago.

Description

ImageJ's support for virtual stacks has been steadily improving. As of the latest version, it would be easy for us to support using them directly through a simple VirtualStack subclass. By overriding the getProcessor(n), getWidth(), getHeight() and getSize() methods to delegate to a Bio-Formats IFormatReader object, we can combine the power of Bio-Formats's per-plane disk reads with ImageJ's native virtual stack logic.

Note that while this will be simple to do, it is no substitute for the Bio-Formats caching logic, since ImageJ's virtual stacks keep only a single plane in memory at a time.

We could actually also combine the caching logic with this VirtualStack subclass to cache ImageProcessor objects according to the user-selected strategy. However, I believe ImageJ would still drop any processing done any time the current plane changes. It is worth investigating.

#551 fixed "waitTime" not parsed from Prairie datasets melissa melissa

Reported by melissa, 9 years ago.

Description

The "waitTime" key in the .cfg file should be parsed into both the original metadata hashtable and Pixels.TimeIncrement.

#622 invalid .aim to TIFF conversion is not quite right melissa melissa

Reported by melissa, 9 years ago.

Description

Specifically:

> 1. The depth of 30205 microns in the original AIM file seems to have been replaced by 863cm, which looks like a 1cm/plane conversion.
> 
> 2. The voxel size has gone from 35 micron^3 to 0.00x0.00x1cm - rounding error, or something else?
> 
> 3 The display range has been changed, going from -7805 - 32767 in the original to  -2220  - 19609 in the tif. 
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