PNG vs TIFF Formats

[Steven Samuelsson]

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May I query the listserv for guidance on which file format is best for converting proprietary .czi and .lif micrographs.  Clearly, am looking for best quality.  Thanks so much.

Steven

[Michael Giacomelli-2]

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Hi Steven,

PNG is lossless and highly compatible (for 8 bit per channel data anyway, 16 bit per channel data can be hit or miss), so I often prefer it.  Unfortunately it is an extremely slow format which makes it very painful for things like whole slide images.  In one script I wrote rotating and converting WSIs to PNG, the PNG encoder alone was more CPU time than all other processing combined.

TIFF is a more complex format that supports a lot more types of compression than PNG, but tends to have compatibility issues, especially for large files because the format is less commonly used and often poorly tested.  The current release of Matlab for instance cannot read its own TIFF files if the file size becomes too large.  This makes working with TIFF much more annoying, but it is often a better idea than PNG, especially for larger files when PNG is too slow to be practical.

Assuming you use lossless TIFF and set the bits per pixel correctly, there will be no difference in the output between PNG and TIFF, only in how compatible and efficient they are.

Mike

On Tue, Jun 4, 2019 at 4:02 PM Steven Samuelsson <[hidden email]<mailto:[hidden email]>> wrote:
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May I query the listserv for guidance on which file format is best for converting proprietary .czi and .lif micrographs.  Clearly, am looking for best quality.  Thanks so much.

Steven

[lechristophe]

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Hi,

Compressed PNG is usually lossless, and tiff is uncompressed, so the
quality will be the same, with a smaller size for PNG. However, metadata is
better preserved with tiff (such as ImageJ metadata: spatial scale,
acquisition parameters...) so I'd advise to store tiff rather than PNG.

Christophe

On Tue, 4 Jun 2019 at 22:02, Steven Samuelsson <[hidden email]>
wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> May I query the listserv for guidance on which file format is best for
> converting proprietary .czi and .lif micrographs.  Clearly, am looking for
> best quality.  Thanks so much.
>
> Steven
>

[Carol Heckman]

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Steven,

TIFF is not a single format but a vast variety of formats, depending on what is in the header and how many bits in which the information from each pixel is encoded.  It is often not readable by software not used for its collection.  As mentioned by somebody already, it is often convertible if you have saved an image as a lossless file.  Even then, the new software may misplace some bits and you get image data that is not suitable for quantitative comparisons.  These comments are a pretty perfunctory analysis, but we teach whole course in this subject!

Carol Heckman

Bowling Green State University


________________________________
From: Confocal Microscopy List <[hidden email]> on behalf of Steven Samuelsson <[hidden email]>
Sent: Tuesday, June 4, 2019 3:48 PM
To: [hidden email]
Subject: [EXTERNAL] PNG vs TIFF Formats

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May I query the listserv for guidance on which file format is best for converting proprietary .czi and .lif micrographs.  Clearly, am looking for best quality.  Thanks so much.

Steven

[Reece, Jeff (NIH/NIDDK) [E]-2]

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Has anyone mentioned OME TIFF yet?  Most of the microscope/acquisition info is retained in the header, which is useful for some microscopy-oriented software; and the result is also still a TIFF, so it is also usually readable by most non-microscopy programs (others can add their experience here).
https://docs.openmicroscopy.org/ome-model/5.6.3/ome-tiff/
It is relatively easy to set up a macro in ImageJ/Fiji to do the conversion quickly.

Cheers,
Jeff

-----Original Message-----
From: Steven Samuelsson <[hidden email]>
Sent: Tuesday, June 4, 2019 3:49 PM
To: [hidden email]
Subject: PNG vs TIFF Formats

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May I query the listserv for guidance on which file format is best for converting proprietary .czi and .lif micrographs.  Clearly, am looking for best quality.  Thanks so much.

Steven