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Hi
Thanks for this resource - it looks really helpful. However, I have repeatedly faced the following error messages when attempting to use.
When using the default configuration I get this error when running with 0.4 um pixel size selected, but not with larger sizes. I tried a fresh reinstall of ImageJ without success:
[INFO] Run NDPI batch converter
NDPIReader initializing C:\Temp\S02_09.06.39\2025-01-18 09.06.39-CY5.ndpi
Reading IFDs
Populating metadata
Populating OME metadata
NDPIReader initializing C:\Temp\S02_09.06.39\2025-01-18 09.06.39-CY5.ndpi
Reading IFDs
Populating metadata
Populating OME metadata
[INFO] Converting:
[INFO] C:\Temp\S02_09.06.39\2025-01-18 09.06.39-CY5.ndpi
[INFO] C:\Temp\S02_09.06.39\2025-01-18 09.06.39-FITC.ndpi
[INFO] C:\Temp\S02_09.06.39\2025-01-18 09.06.39-TRITC.ndpi
[INFO] to: C:\Temp\S02_09.06.39\2025-01-18 09.06.39-CY5_series-1.ome.tif
NDPIReader initializing C:\Temp\S02_09.06.39\2025-01-18 09.06.39-CY5.ndpi
Reading IFDs
Populating metadata
Populating OME metadata
Switching to BigTIFF (by file size)
NDPIReader initializing C:\Temp\S02_09.06.39\2025-01-18 09.06.39-CY5.ndpi
[ERROR] Command errored: Batch OME-TIF Converter
java.lang.ArrayIndexOutOfBoundsException
at java.lang.System.arraycopy(Native Method)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:219)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:153)
at NdpiUtils.convert(NdpiUtils.java:169)
at BatchConverter.run(BatchConverter.java:87)
at org.scijava.command.CommandModule.run(CommandModule.java:196)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:125)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:64)
at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:247)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:750)
The text was updated successfully, but these errors were encountered:
Hi
Thanks for this resource - it looks really helpful. However, I have repeatedly faced the following error messages when attempting to use.
When using the default configuration I get this error when running with 0.4 um pixel size selected, but not with larger sizes. I tried a fresh reinstall of ImageJ without success:
[INFO] Run NDPI batch converter
NDPIReader initializing C:\Temp\S02_09.06.39\2025-01-18 09.06.39-CY5.ndpi
Reading IFDs
Populating metadata
Populating OME metadata
NDPIReader initializing C:\Temp\S02_09.06.39\2025-01-18 09.06.39-CY5.ndpi
Reading IFDs
Populating metadata
Populating OME metadata
[INFO] Converting:
[INFO] C:\Temp\S02_09.06.39\2025-01-18 09.06.39-CY5.ndpi
[INFO] C:\Temp\S02_09.06.39\2025-01-18 09.06.39-FITC.ndpi
[INFO] C:\Temp\S02_09.06.39\2025-01-18 09.06.39-TRITC.ndpi
[INFO] to: C:\Temp\S02_09.06.39\2025-01-18 09.06.39-CY5_series-1.ome.tif
NDPIReader initializing C:\Temp\S02_09.06.39\2025-01-18 09.06.39-CY5.ndpi
Reading IFDs
Populating metadata
Populating OME metadata
Switching to BigTIFF (by file size)
NDPIReader initializing C:\Temp\S02_09.06.39\2025-01-18 09.06.39-CY5.ndpi
[ERROR] Command errored: Batch OME-TIF Converter
java.lang.ArrayIndexOutOfBoundsException
at java.lang.System.arraycopy(Native Method)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:219)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:153)
at NdpiUtils.convert(NdpiUtils.java:169)
at BatchConverter.run(BatchConverter.java:87)
at org.scijava.command.CommandModule.run(CommandModule.java:196)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:125)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:64)
at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:247)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:750)
The text was updated successfully, but these errors were encountered: