Can't open files acquired at MetaXpress

bio-formats
#1

Hi all,

We’re trying to automate things at the MetaXpress microscope but I’m facing issues with opening the images using Bio-Formats.

It fails when opening the HTD files in Fiji (using the Bio-Formats plugin) but it works when using one of the two tif files. Do you have any ideas why ?

Here is the error I’m getting:

loci.formats.FormatException: Invalid image number: 1 (series=0, imageCount=1)
	at loci.formats.FormatTools.checkPlaneNumber(FormatTools.java:1009)
	at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:997)
	at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
	at loci.formats.in.MetamorphReader.openBytes(MetamorphReader.java:285)
	at loci.formats.in.CellWorxReader.openBytes(CellWorxReader.java:201)
	at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:156)
	at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
	at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334)
	at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:233)
	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334)
	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334)
	at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:186)
	at loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:422)
	at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:387)
	at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:282)
	at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:243)
	at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:221)
	at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:116)
	at loci.plugins.in.Importer.readPixels(Importer.java:149)
	at loci.plugins.in.Importer.run(Importer.java:86)
	at loci.plugins.LociImporter.run(LociImporter.java:78)
	at ij.IJ.runUserPlugIn(IJ.java:229)
	at ij.IJ.runPlugIn(IJ.java:193)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at ij.IJ.run(IJ.java:309)
	at ij.IJ.run(IJ.java:320)
	at ij.macro.Functions.doRun(Functions.java:623)
	at ij.macro.Functions.doFunction(Functions.java:97)
	at ij.macro.Interpreter.doStatement(Interpreter.java:270)
	at ij.macro.Interpreter.doStatements(Interpreter.java:256)
	at ij.macro.Interpreter.run(Interpreter.java:152)
	at ij.macro.Interpreter.run(Interpreter.java:91)
	at ij.macro.MacroRunner.run(MacroRunner.java:139)
	at java.lang.Thread.run(Thread.java:748)

Thanks a lot.

KaisMagicPlate_plt-1_ts-002583D7x03873418.zip (1.2 MB)

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#2

Hi @lguerard

Can you explain more about what failure you are seeing? Optimal is if you can include the error output here.

Thanks,
~Josh

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#3

My bad ! I edited the post with the error from Fiji !

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#4

From the HTD file you posted:

"TimePoints", 2

"XWells", 3

"YWells", 2

… but you only provide 2 tiff files. It seems the dataset is incomplete, no?

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#5

Hi @imagejan,

Thanks for pointing it out, the software is stupid enough to actually write the number of wells in X and Y for the plate not caring about how many you used. I will need to find a way to change that.

However, I just tried changing it to 1 and 1 and the issue is still there.

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#6

Hi @lguerard, using the sample fileset you attached and the latest Bio-Formats (6.0.1) I was able to open the HTD file without the exception. What version are you currently using?

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#7

Hi !

I have the exact same version somehow.

image

Do you open directly the HTD file in Fiji ? Because opening the images work fine, just not the HTD somehow… :confused:

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#8

Yeah I was able to open using the HTD directly. The error you are seeing suggests that it has perhaps been unsuccessful in locating the second file for some reason. Is there anything different in the file structure compared to the zipped folder? Are you using Windows, Mac etc?

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#9

Not at all, it’s the same files in the same folder with the same name. I even tried redownloading the ZIP above to check and it’s the same.

I tried on Linux (Mint) and on Windows 7 with the same issue…

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#10

I retested with the Bio-Formats command line tools (6.0.1 as well) and am now reproducing the exact same error as you had. I will try and further debug the problem to see what the cause is.

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