Ticket #388 (closed defect: fixed)

I have found the reason why the metadata is not correctly extracted from the FLEX file.

In: loci.formats.in.FlexReader.java Line: 372-376

else if (currentQName.equals("LightSourceCombinationRef")) {

if (!channelNames.contains(value) && lightSourceIDs.contains(value)) {

channelNames.add(value);

}

}

This referes to the light source combination. Currently the Opera supports only 1 or 2 light source combination. The light source combination simply indicates which lasers are on for the given exposures (currently max# of exposure=2). For each light source combination there will be a filtercombination. In each filter combination, there might be up to 4 Cameras activated. Hence in order to know how many Channels there are, one need to iterate over the filter combination and count oh many time a slider name camera is present.

Following XML extract might be helpful:

<FilterCombinations>

<FilterCombination ID="F_Sample_1">

<SliderRef ID="Camera1" Filter="535/50" /> <SliderRef ID="Camera2" Filter="690/50" /> <SliderRef ID="Primary_Dichro" Filter="488" /> <SliderRef ID="Detect_Dichro" Filter="580" />

</FilterCombination>

</FilterCombinations>

Alternativelly, another method is to count in the Array section how many Name tye there are (ex "Exp1Cam1", "Exp2Cam2 etc.) The following portion of the Header is useful: <Arrays>

<Array Type="Image" Name="Exp1Cam1" Width="608" Height="456"

BitsPerPixel="16" CompressionType="" CompressionRate="" Factor="1.000000" />

<Array Type="Image" Name="Exp1Cam3" Width="608" Height="456"

BitsPerPixel="16" CompressionType="" CompressionRate="" Factor="1.000000" />

Here is an exert of the XML header.