CZI from AxioScan does not open correctly with BioFormtas 6.1.1

[sebi06]

Hi,

I have a CZI that does open correctly with BioFormats 6.1.1. I did the following

• open compressed CZI in Fiji
• open uncompressed CZI in Fiji
• export CZI as OME-TIFF from ZEN and open in Fiji
• export CZI as BigTIFF from ZEN and open in Fiji

None of those approached works correctly. But when I open the BigTIFF inside another (non-BioFormats based viewer) it open correctly without artifacts, which makes we wonder, if this a bug in BioFormats.

At the very bottom I also attached a screenshot of ZEN and the llink to the CZI:

https://www.dropbox.com/s/5guj227wt7spk1l/2019_06_21__13_01__0095.czi?dl=0

[mtbc]

Thank you, sample files and corresponding screenshots are always helpful. I've now placed 2019_06_21__13_01__0095.czi where the Bio-Formats team can experiment with it.

[sebi06]

No problem. Let me know if your need more info. We really need to sort this out since the user (are understandably) quite unhappy with this ....

[dgault]

Hi @sebi06, I have been testing the submitted file today and so far I've not been able to reproduce the issue. Do you still see the issue if you use the showinf command line tool? (https://www.openmicroscopy.org/bio-formats/downloads/, docs on the showinf command - https://docs.openmicroscopy.org/bio-formats/6.1.1/users/comlinetools/display.html)

Im wondering if it is perhaps related to https://forum.image.sc/t/polygon-tool-distorts-series-read-into-fiji-via-the-bio-formats-importer-plugin/27249

[sebi06]

I just tried it out at home on Ubuntu and got stuck here:

(base) sebi06@sebastian-tuxedo:/datadisk1/tuxedo/BioFormats/6.1.1$ java -XshowSettings:vm VM settings: Max. Heap Size (Estimated): 7.79G Using VM: Java HotSpot(TM) 64-Bit Server VM

So i figured this should be OK for an 180MB CZI file, but it turns out it is not ... But I do not really know yet, how to adress this issue.

(base) sebi06@sebastian-tuxedo:/datadisk1/tuxedo/BioFormats/6.1.1$ bash showinf /datadisk1/Sebastian/Dropbox/CZI_Testdata/2019_06_2113_01__0095.czi Checking file format [Zeiss CZI] Initializing reader ZeissCZIReader initializing /datadisk1/Sebastian/Dropbox/CZI_Testdata/2019_06_2113_01__0095.czi Initialization took 1.935s

Reading core metadata filename = /datadisk1/Sebastian/Dropbox/CZI_Testdata/2019_06_21__13_01__0095.czi Series count = 8 Series #0 : Image count = 1 RGB = true (3) Interleaved = true Indexed = false (false color) Width = 18935 Height = 30364 SizeZ = 1 SizeT = 1 SizeC = 3 (effectively 1) Tile size = 1024 x 1024 Thumbnail size = 79 x 128 Endianness = intel (little) Dimension order = XYCZT (certain) Pixel type = uint8 Valid bits per pixel = 8 Metadata complete = false Thumbnail series = false

Plane #0 <=> Z 0, C 0, T 0

Series #1 : Image count = 1 RGB = true (3) Interleaved = true Indexed = false (false color) Width = 9467 Height = 15182 SizeZ = 1 SizeT = 1 SizeC = 3 (effectively 1) Tile size = 1024 x 1024 Thumbnail size = 79 x 128 Endianness = intel (little) Dimension order = XYCZT (certain) Pixel type = uint8 Valid bits per pixel = 8 Metadata complete = false Thumbnail series = false

Plane #0 <=> Z 0, C 0, T 0

Series #2 : Image count = 1 RGB = true (3) Interleaved = true Indexed = false (false color) Width = 4733 Height = 7591 SizeZ = 1 SizeT = 1 SizeC = 3 (effectively 1) Tile size = 1024 x 1024 Thumbnail size = 79 x 128 Endianness = intel (little) Dimension order = XYCZT (certain) Pixel type = uint8 Valid bits per pixel = 8 Metadata complete = false Thumbnail series = false

Plane #0 <=> Z 0, C 0, T 0

Series #3 : Image count = 1 RGB = true (3) Interleaved = true Indexed = false (false color) Width = 2366 Height = 3795 SizeZ = 1 SizeT = 1 SizeC = 3 (effectively 1) Tile size = 1024 x 1024 Thumbnail size = 79 x 128 Endianness = intel (little) Dimension order = XYCZT (certain) Pixel type = uint8 Valid bits per pixel = 8 Metadata complete = false Thumbnail series = false

Plane #0 <=> Z 0, C 0, T 0

Series #4 : Image count = 1 RGB = true (3) Interleaved = true Indexed = false (false color) Width = 1183 Height = 1897 SizeZ = 1 SizeT = 1 SizeC = 3 (effectively 1) Tile size = 1024 x 1024 Thumbnail size = 79 x 128 Endianness = intel (little) Dimension order = XYCZT (certain) Pixel type = uint8 Valid bits per pixel = 8 Metadata complete = false Thumbnail series = false

Plane #0 <=> Z 0, C 0, T 0

Series #5 : Image count = 1 RGB = true (3) Interleaved = true Indexed = false (false color) Width = 591 Height = 948 SizeZ = 1 SizeT = 1 SizeC = 3 (effectively 1) Tile size = 591 x 948 Thumbnail size = 79 x 128 Endianness = intel (little) Dimension order = XYCZT (certain) Pixel type = uint8 Valid bits per pixel = 8 Metadata complete = false Thumbnail series = false

Plane #0 <=> Z 0, C 0, T 0

Series #6 : Image count = 1 RGB = true (3) Interleaved = true Indexed = false (false color) Width = 518 Height = 668 SizeZ = 1 SizeT = 1 SizeC = 3 (effectively 1) Tile size = 518 x 337 Thumbnail size = 99 x 128 Endianness = intel (little) Dimension order = XYCZT (certain) Pixel type = uint16 Valid bits per pixel = 12 Metadata complete = false Thumbnail series = true

Plane #0 <=> Z 0, C 0, T 0

Series #7 : Image count = 1 RGB = true (3) Interleaved = true Indexed = false (false color) Width = 1500 Height = 723 SizeZ = 1 SizeT = 1 SizeC = 3 (effectively 1) Tile size = 1500 x 116 Thumbnail size = 128 x 61 Endianness = intel (little) Dimension order = XYCZT (certain) Pixel type = uint16 Valid bits per pixel = 12 Metadata complete = false Thumbnail series = true

Plane #0 <=> Z 0, C 0, T 0

Reading series #0 pixel data (0-0) Exception in thread "main" java.lang.OutOfMemoryError: Java heap space at loci.common.DataTools.allocate(DataTools.java:1260) at loci.formats.FormatReader.openBytes(FormatReader.java:869) at loci.formats.ImageReader.openBytes(ImageReader.java:445) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:86) at loci.formats.tools.ImageInfo.readPixels(ImageInfo.java:821) at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:1055) at loci.formats.tools.ImageInfo.main(ImageInfo.java:1121) (base) sebi06@sebastian-tuxedo:/datadisk1/tuxedo/BioFormats/6.1.1$

[sebi06]

And when I try to open the CZI on the same system with Fiji I get no java heap spcae issues. The image at first glance looks also distorted. But when I then run split channels on the image with the aritfacts the resulting 3 channel look OK - ???