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Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
https://www.openmicroscopy.org/bio-formats
GNU General Public License v2.0
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CZI: Autostich fails #4102

Open dgault opened 1 year ago

dgault commented 1 year ago

Issue was raised on forum thread https://forum.image.sc/t/zoom-from-overview-to-detailed-scan-for-imported-czi-files/85002/6

A sample was provided that reproduces the issue with Bio-Formats 7.0.0 - https://zenodo.org/record/8423633

When opening the file, even with the autostitch option selected, the file opens as 36 individual series. This appears to be 5 tiles, most of which have 7 resolutions, but 1 has 6 resolutions, the sizes of these 6 resolutions do not match the other 4. There is also an additional label and macro attachment image.

When using the noflat option it is returning 7 series as below:

Series count = 7
Series #0 :
    Resolutions = 7
        sizeX[0] = 33309
        sizeX[1] = 16654
        sizeX[2] = 8327
        sizeX[3] = 4163
        sizeX[4] = 2081
        sizeX[5] = 1040
        sizeX[6] = 520
    Image count = 1
    RGB = true (3) 
    Interleaved = true
    Indexed = false (false color)
    Width = 33309
    Height = 29285
    SizeZ = 1
    SizeT = 1
    SizeC = 3 (effectively 1)
    Tile size = 1024 x 1024
    Thumbnail size = 128 x 112
    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 :
    Resolutions = 7
        sizeX[0] = 33357
        sizeX[1] = 16678
        sizeX[2] = 8339
        sizeX[3] = 4169
        sizeX[4] = 2084
        sizeX[5] = 1042
        sizeX[6] = 521
    Image count = 1
    RGB = true (3) 
    Interleaved = true
    Indexed = false (false color)
    Width = 33357
    Height = 29295
    SizeZ = 1
    SizeT = 1
    SizeC = 3 (effectively 1)
    Tile size = 1024 x 1024
    Thumbnail size = 128 x 112
    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 :
    Resolutions = 7
        sizeX[0] = 33331
        sizeX[1] = 16665
        sizeX[2] = 8332
        sizeX[3] = 4166
        sizeX[4] = 2083
        sizeX[5] = 1041
        sizeX[6] = 520
    Image count = 1
    RGB = true (3) 
    Interleaved = true
    Indexed = false (false color)
    Width = 33331
    Height = 20698
    SizeZ = 1
    SizeT = 1
    SizeC = 3 (effectively 1)
    Tile size = 1024 x 1024
    Thumbnail size = 128 x 79
    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 :
    Resolutions = 6
        sizeX[0] = 26093
        sizeX[1] = 13046
        sizeX[2] = 6523
        sizeX[3] = 3261
        sizeX[4] = 1630
        sizeX[5] = 815
    Image count = 1
    RGB = true (3) 
    Interleaved = true
    Indexed = false (false color)
    Width = 26093
    Height = 5576
    SizeZ = 1
    SizeT = 1
    SizeC = 3 (effectively 1)
    Tile size = 1024 x 1024
    Thumbnail size = 128 x 27
    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 :
    Resolutions = 7
        sizeX[0] = 34784
        sizeX[1] = 17392
        sizeX[2] = 8696
        sizeX[3] = 4348
        sizeX[4] = 2174
        sizeX[5] = 1087
        sizeX[6] = 543
    Image count = 1
    RGB = true (3) 
    Interleaved = true
    Indexed = false (false color)
    Width = 34784
    Height = 24965
    SizeZ = 1
    SizeT = 1
    SizeC = 3 (effectively 1)
    Tile size = 1024 x 1024
    Thumbnail size = 128 x 91
    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 = 698
    Height = 649
    SizeZ = 1
    SizeT = 1
    SizeC = 3 (effectively 1)
    Tile size = 12 x 9
    Thumbnail size = 128 x 119
    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 #6 :
    Image count = 1
    RGB = true (3) 
    Interleaved = true
    Indexed = false (false color)
    Width = 1458
    Height = 777
    SizeZ = 1
    SizeT = 1
    SizeC = 3 (effectively 1)
    Tile size = 1458 x 119
    Thumbnail size = 128 x 68
    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
imagesc-bot commented 1 year ago

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/zoom-from-overview-to-detailed-scan-for-imported-czi-files/85002/8

imagesc-bot commented 1 year ago

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/pb-when-i-open-czi-stitching-image/87585/3

dgault commented 1 year ago

Another auto-stitching issue has been reported on forum thread https://forum.image.sc/t/pb-when-i-open-czi-stitching-image/87585/2

A sample image was provided and is available at inbox/imagesc-87585 and the issue can be reproduced using Bio-Formats 7.0.1 with the CZI auto-stitching option enabled.

In this particular case the user was able to save a stitched image with Zen 3.4 and that opens as expected, but when saved with Zen 3.8 the image appears "distorted" with the stitching option enabled. In QuPath zooming in to the highest resolution level produced a normal looking image, similarly cropping regions of the highest resolution also seemed to return correct looking pixel data. When the stitching option is disabled the individual tiles appear to be correct and display as expected.

imagesc-bot commented 1 year ago

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/pb-when-i-open-czi-stitching-image/87585/9

dgault commented 1 year ago

Additional sample files have been provided that are now included in inbox/imagesc-87585

imagesc-bot commented 9 months ago

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/pb-when-i-open-czi-stitching-image/87585/27

dgault commented 9 months ago

The issue reported in https://github.com/ome/bioformats/issues/4102#issuecomment-1772752535 appears to be different to that in the original Issue description. I am splitting this report into a new seperate Issue https://github.com/ome/bioformats/issues/4150 which is addressed by https://github.com/ome/bioformats/pull/4138

imagesc-bot commented 9 months ago

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/zoom-from-overview-to-detailed-scan-for-imported-czi-files/85002/25

MichaelDausmann commented 9 months ago

I have done additional research on this issue.

TLDR, I don't think the AutoStitch option is stitching scenes together.

a ‘Scene’ in CZI is represented by the ‘S’ Dimension. according to the documentation,

And we have the letter ‘S’ in use, and it is used in the following way: sub-blocks with the same S-index form a set called “scene”. A scene is a rectangular (and axis aligned) region, and much like the bounding box, it is determined by taking all planes into consideration.

In the ZeissCZIReader, as best as i can tell, the ‘S’ dimension is being interpreted as a ‘Series’ dimension.

For context, I have attached the output of the CZIcmd utility for my test file... stitching_testfile_czicmdoutput.txt Note that the file is arranged into 5 Scenes, each with their own pyramids.

I have also attached a detailed dump of all the subblocks in my test file... stitching_subblocks_detail.txt

I also have been able to debug through ZeissCZIReader.java as it reads my file autostitch_not_stitching_scenes

I noticed that despite autostitching being on by default, the sub-blocks in Scenes > 0 are being placed into seperate series e.g. block at i=489 ends up in Series 28.

Whether Autostitch ignoring scenes or the interpretation of 'S' as a 'Series' rather than a 'Scene' was intentional, I can't tell.

I guess what I am asking is either through an additional option or by default, the 'S' Dimension should be ignored from a Series perspective so that all sub-blocks in my file with the same scale (zoom, z) end up in the same series. that would mean for my test file I would end up with 9 series rather than 36 i.e. 7 series with all of the tiles from the pyramids, and one series each for the slide header and the macro view.

I think as a 'feature', this would mean that a multi-scene .czi file would be imported e.g into Omero as a 'whole slide' image rather than an image per scene.

Hope this makes sense

MichaelDausmann commented 5 months ago

@dgault recommend closure of this ticket in favour of https://github.com/ome/bioformats/issues/4194