Open Keyence .tif and .ktf file formats in Fiji?

Usage & Issues
#1

Greetings everyone,
We are using a Keyence BZ-X800 microscope to acquire many tiled images and tiled image z-stacks. Sadly, I have not found a way to use the Bio-formats file loaders to access these images in Fiji.

We can load individual .tif files but without metadata. We can also load the .tif files for each z-stack, but without the metadata which would need to be added manually. Any advice on how to get Bioformats to access the metadata or to directly load Keyence .tif and .ktf files or to load the .gci which appears to contains stack meta data in xml format)? Suggestions are welcome.
Thanks
-Chris Leonard

#2

Hi Chris,

Im afraid the Keyence .ktf format is not yet supported in Bio-Formats. You can read more on the current position of OME and file formats in this blog post: https://blog.openmicroscopy.org/community/file-formats/2019/06/25/formats/

I have opened a Trello card on the Bio-Formats New Formats board to track your interest in this format: https://trello.com/c/QB2c5x5I/52-keyence-ktf

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#3

Hi David,

Thanks for your response and for the link to the blog post concerning format support. I was unaware of this sensible view. I will bug keyence some more about these issues. It would help enormously if we could assess the metadata in imageJ.

RE: the trello card, should I elaborate on our use for the .kft format or is this just for internal record keeping? What do you mean by “track my interest”?

Thanks again for all your great work!

-Chris

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#4

The Trello cards are more for internal use so we can keep track of how many requests we have had for various different formats. The community is more than welcome to comment on the cards or add details but it is not required.

#5

I’ve had a similar issue trying to extract the metadata from .tif files made with a BZ-X800 microscope. Turns out the XML for the metadata is appended to the end of the .tif file. If you’re Linux-savvy, try grep -a -e"" -B0 -A1000 Image_0001.tif to extract all the XML.

#6

Seem to have lost something in translation. Try:

grep -a -e"Data" -B0 -A1000 Image_0001.tif

#7

I have a different question about .ktf files… with what do you open them at all to see them?

#8

Hi @dgault Has there been any more discussion of adding .ktf file support for Bio-Formats? I know the BZ-X800 series has been a pretty popular instrument and people would love to be able to work with images and metadata in ImageJ/Fiji. Thanks for all your hard work on making this tool available for us.

#9

Hi @Andrew_Hardaway, realistically the open source team has not had the resources or funding to keep pace with the development of proprietary formats and have been focused on adding support for the next generation of open formats. Ideally vendors would also provide customers with support for open formats, alternatively we have seen 3i for example who have taken ownership of providing a reader for their formats or other companies who have commissioned support for formats via Glencoe Software.

The blog posts https://blog.openmicroscopy.org/file-formats/community/2016/01/06/format-support/ and more recently https://blog.openmicroscopy.org/community/file-formats/2019/06/25/formats/ covers our position in more detail

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#10

Hi. Thank you for your response. I totally understand that position. I’ll talk to Keyence and report back. I’m sure they would prefer people use their proprietary software but you never know. I’ll report back what I hear.

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#11

Hi Alan,
I’m embarrassed to say I have only just tried this. This works fine in the Mac version of grep too. This provides some good info like Lens Type, exposure time; camera gain and camera hardware gain.

I could not find information about spatial calibration however. Any idea how to get micron/px? I see 6000 This image was take with a 60x dry plan apo. Not sure how to convert this to micron/px

Thanks again!

#12

Hi @Andrew_Hardaway, I do not suppose you had any luck? I have someone bringing metadata free .tif files from a Keyence, and would be curious if there is any hope on this front. Otherwise we can just ask them to rescan on a Zeiss or Hamamatsu scanner.

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