Opening different video types with Bio-Formats Importer in Fiji

[GrossLab]

Hello,

We are developing a Nextflow pipeline for image processing with some Fiji scripts and we are having troubles opening our video files with the Bio-Formats Importer.
More specifically, we need work with both .tif and .tiff files, which sometimes appear as TIFF, other times as BigTiff.

(base) [torchia@login2 Valeria]$ file *.tif*
concatenated_video_subset.tif:       TIFF image data, big-endian, direntries=13, height=0, bps=16, compression=none, PhotometricIntepretation=BlackIsZero, description=ImageJ=1.54p, width=0
concatenated_video.tif:              TIFF image data, big-endian, direntries=13, height=0, bps=16, compression=none, PhotometricIntepretation=BlackIsZero, description=ImageJ=1.54p, width=0
FLPGAT250423B_day2.tiff:             TIFF image data, big-endian, direntries=13, height=0, bps=16, compression=none, PhotometricIntepretation=BlackIsZero, description=ImageJ=1.54f, width=0
FLPGLUT250710_d123.tif:              Big TIFF image data, big-endian
FLPGLUT250710_d123.tiff:             Big TIFF image data, little-endian
NGLUT240415_social_D1_D2_subset.tif: TIFF image data, big-endian, direntries=13, height=0, bps=16, compression=none, PhotometricIntepretation=BlackIsZero, description=ImageJ=1.54f, width=0
NGLUT250227_hab3.tif:                TIFF image data, big-endian, direntries=14, height=0, bps=16, compression=none, PhotometricIntepretation=BlackIsZero, description={"shape": [9391, 375, 400]}, width=0
NGLUT250227_hab3.tiff:               Big TIFF image data, little-endian

The video size varies as well:

(base) [torchia@login2 Valeria]$ ls -l --human-readable
-rw-r--r-- 1 torchia gross 566M Jul 15 13:51 concatenated_video_subset.tif
-rw-r--r-- 1 torchia gross  21G Apr 15 11:43 concatenated_video.tif
-rw-r--r-- 1 torchia gross 5.1G Aug 22 11:06 FLPGAT250423B_day2.tiff
-rwxr-xr-x 1 torchia gross  11G Oct  8 11:37 FLPGLUT250710_d123.tif
-rwxr-xr-x 1 torchia gross  12G Sep 25 19:14 FLPGLUT250710_d123.tiff
-rw-r--r-- 1 torchia gross 406M Oct  3  2024 NGLUT240415_social_D1_D2_subset.tif
-rw-r--r-- 1 torchia gross 2.7G Aug  1 12:15 NGLUT250227_hab3.tif
-rwxr-xr-x 1 torchia gross 2.7G May 27 14:24 NGLUT250227_hab3.tiff

Is there a way to open all these videos with run("Bio-Formats Importer") ?

Thank you so much,

Sofia

[melissalinkert]

In principle, I'd expect TIFF and BigTIFF to be well supported by Bio-Formats. Are you seeing error messages when you try to open some of these files? If so, what are the complete error messages (and which version of Bio-Formats is installed)? Are you able to upload any of the files that do not open to https://zenodo.org/communities/bio-formats/records?

[GrossLab]

Hello,

Thank you so much for your quick response. Can I get back to you in a couple of days to see whether I can upload the file in the link you send? In the meantime can tell you more about our issue.

This is the Fiji script where we only try to open the file (I removed the rest of the script to isolate the problem):

(base) [torchia@login2 fiji]$ cat background_subtraction_openimage.ijm
// Get the input image path from the command line argument
input = getArgument();

run("Bio-Formats Importer", "open=" + input + " open_all_series windowless=true");

// Verify an image opened
if (nImages == 0) {
    print("ERROR: no images opened for " + input);
    exit();
} else {
    print("Number of images opened: " + nImages);
}
(base) [torchia@login2 fiji]$ module load fiji

Here I run the script on FLPGLUT250710_d123.tif:

 module load fiji
(base) [torchia@login2 fiji]$ ImageJ-linux64 --headless --console -macro background_subtraction_openimage.ijm ../../../Valeria/FLPGLUT250710_d123.tif
OpenJDK 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
OpenJDK 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
java.lang.VerifyError: Bad type on operand stack
Exception Details:
  Location:
    loci/plugins/in/MainDialog.rebuildDialog(Lij/gui/GenericDialog;)V @1926: invokestatic
  Reason:
    Type 'ij/gui/GenericDialog' (current frame, stack[0]) is not assignable to 'java/awt/Container'
  Current Frame:
    bci: @1926
    flags: { }
    locals: { 'loci/plugins/in/MainDialog', 'ij/gui/GenericDialog', 'java/util/List', 'java/util/List', 'java/util/List', 'java/awt/Label', 'java/awt/Label', 'java/awt/Label', 'java/awt/Label', '[Ljava/awt/Component;', 'java/lang/String', 'java/lang/String', 'com/jgoodies/forms/builder/PanelBuilder', 'com/jgoodies/forms/layout/CellConstraints', integer }
    stack: { 'ij/gui/GenericDialog' }
  Bytecode:
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    0x0000580: 0415 0e06 b700 99b6 0097 5784 0e02 190c
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    0x00005a0: 9757 840e 0219 0c12 9a19 0d04 150e 06b6
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    0x00005d0: 0d06 150e b600 96b6 0097 5784 0e02 190c
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    0x00005f0: 9757 840e 0204 360e 190c 129b 190d 0815
    0x0000600: 0e06 b600 94b6 0095 5784 0e02 190c 2ab4
    0x0000610: 0068 2a19 0d08 150e 06b7 0099 b600 9757
    0x0000620: 840e 0219 0c2a b400 692a 190d 0815 0e06
    0x0000630: b700 99b6 0097 5784 0e02 190c 2ab4 006a
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    0x0000790: b1
  Stackmap Table:
    full_frame(@58,{Object[#309],Object[#310],Object[#311],Object[#311],Object[#311],Object[#312],Object[#312],Object[#312],Object[#312],Object[#313],Integer},{})
    same_frame(@117)
    same_frame(@168)
    same_frame(@195)
    chop_frame(@201,1)
    same_frame_extended(@641)

        at loci.plugins.in.ImporterPrompter.promptMain(ImporterPrompter.java:132)
        at loci.plugins.in.ImporterPrompter.statusUpdated(ImporterPrompter.java:79)
        at loci.plugins.in.ImportProcess.notifyListeners(ImportProcess.java:476)
        at loci.plugins.in.ImportProcess.step(ImportProcess.java:772)
        at loci.plugins.in.ImportProcess.execute(ImportProcess.java:140)
        at loci.plugins.in.Importer.showDialogs(Importer.java:140)
        at loci.plugins.in.Importer.run(Importer.java:76)
        at loci.plugins.LociImporter.run(LociImporter.java:78)
        at ij.IJ.runUserPlugIn(IJ.java:243)
        at ij.IJ.runPlugIn(IJ.java:204)
        at ij.Executer.runCommand(Executer.java:152)
        at ij.Executer.run(Executer.java:70)
        at ij.IJ.run(IJ.java:325)
        at ij.IJ.run(IJ.java:336)
        at ij.macro.Functions.doRun(Functions.java:703)
        at ij.macro.Functions.doFunction(Functions.java:99)
        at ij.macro.Interpreter.doStatement(Interpreter.java:281)
        at ij.macro.Interpreter.doStatements(Interpreter.java:267)
        at ij.macro.Interpreter.run(Interpreter.java:163)
        at ij.macro.Interpreter.run(Interpreter.java:93)
        at ij.macro.Interpreter.run(Interpreter.java:107)
        at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:162)
        at ij.plugin.Macro_Runner.runMacroFile(Macro_Runner.java:146)
        at ij.IJ.runMacroFile(IJ.java:171)
        at net.imagej.legacy.IJ1Helper$4.call(IJ1Helper.java:1165)
        at net.imagej.legacy.IJ1Helper$4.call(IJ1Helper.java:1161)
        at net.imagej.legacy.IJ1Helper.runMacroFriendly(IJ1Helper.java:1095)
        at net.imagej.legacy.IJ1Helper.runMacroFile(IJ1Helper.java:1161)
        at net.imagej.legacy.LegacyCommandline$Macro.handle(LegacyCommandline.java:185)
        at org.scijava.console.DefaultConsoleService.processArgs(DefaultConsoleService.java:99)
        at org.scijava.AbstractGateway.launch(AbstractGateway.java:103)
        at net.imagej.Main.main(Main.java:55)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:279)
        at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:186)
        at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:87)

ERROR: no images opened for ../../../Valeria/FLPGLUT250710_d123.tif
(base) [torchia@login2 fiji]$

More info on the fiji version:

(base) [torchia@login2 fiji]$ module list

Currently Loaded Modules:
  1) fiji/2024-09-04

Thank you again for your support. Please, let me know if I can provide more information.

Sofia

[GrossLab]

Hi,

Apologies for taking so long to provide the data. You can find some recordings here: https://zenodo.org/records/17339691
Please, let us know if we can provide any other information.
Thank you for your support, we look forward to your answer.

Best regards,
Sofia

[melissalinkert]

Thanks, @GrossLab. I am able to open FLPGLUT250710_d123.tif in an up-to-date Fiji without error, so this doesn't appear to be a problem with the files themselves.

The error message added to #4372 (comment) is consistent with some previously-reported issues with running headless macros, e.g. https://forum.image.sc/t/run-script-headlessly/43488.

If you try replacing this line in the macro:

run("Bio-Formats Importer", "open=" + input + " open_all_series windowless=true");

with these lines:

run("Bio-Formats Macro Extensions");
Ext.openImagePlus(input);

does that work any better? If you still see an error message with that change, please paste the full error here.

https://bio-formats.readthedocs.io/en/latest/users/imagej/index.html#macros-and-plugins has some more information about using Bio-Formats macro extension functions as an alternative to run("Bio-Formats Importer", ...).