SCIFIO needs your sample data

Hi everyone,

I have been working on the next release of scifio:


It includes support for reading from remote locations, bugfixes and more. During development I had to rely on private sample data which is limited and not suitable for public automated testing. By using real data from the public we ensure that scifio actually works in the field.

While I was able to procure and create test data for many formats, I am still looking for sample data from the formats listed bellow. This is where I hope the image.sc community can help me:

Desired Formats
  • DICOM
  • FITS
  • MicroManager 1 & 2
  • MNG
  • NRRD
  • OBF
  • PCX
  • PGM
Sample file requirements

Sample files should be as small as possible while staying representative for the format. For example a 200x200x3x5 image volume is completely sufficient to demonstrate that a certain file type can be read.

All example files will be published on https://scif.io/images/, so they can’t be encumbered by licensing or usage restrictions.

Thank you very much!
Gabriel

4 Likes

Hi Gabriel,

https://scif.io/images/ looks slick! Do any of the images under https://downloads.openmicroscopy.org/images do what you need? We’ve begun asking all bug submitters to provide their images under an open license (see COPYING in each folder) and this is the subset of images used for regression testing of #bio-formats that we can make public.

~Josh

2 Likes

Thank you @joshmoore, looks like I will find a lot of what I need there :slight_smile:
best,
Gabriel

I’d be happy to contribute (to any or both the above repositories) a few Metamorph/VisiView datasets that currently fail with bio-formats (since two years actually):

See the following commit and related issue for how they fail:

Let me know if I need to do anything to have them integrated.

Hi @gab1one,
Thanks for pushing SCIFIO dev forward.
Does this release address the performance issues when reading from ZIP files?
E.g. any 3D stack, saved as a ZIP file a la ImageJ (one 2D slice per ZIP entry), is read fast in ImageJ and several orders of magnitude slower with SCIFIO.
Would be nice to incude any such ZIP file into the SCIFIO test suite.
Thanks,
Albert

1 Like

Hi @imagejan,
there is currently no reader for that format in scifio, so we would need to add one there to fix this issue for you. I do not know when I will have time for that though.
best,
Gabriel

Sadly not, increasing the performance of SCIFIO is planed for the next iteration though, thank you for pointing out this issue.
best,
Gabriel

1 Like

hi @gab1one

I pushed 2 DICOM images which has problem to be read by SCIFIO


And a problem with tag sequences in DICOM

i’m using a lot of DICOM, SCIFIO is of interest for us because it is our hope to see compressed images supported by Fiji.
As now these bugs are preventing us to use SCIFIO as reader but I will do more test when I read DICOM and report to you everytime I see problems

Thanks for your work

Best regards,

Salim

Hi, Do you really mean this PCX format? https://en.wikipedia.org/wiki/PCX
Pretty much replaced by PNG long long time ago. Is anybody still using it?

Thank you for posting them, I will take a look at these and try to get them fixed.

Explains why I was not able to find any examples for it :slight_smile:

I’ve got a QuickBasic (!) version of the 8bit palette PCX reader and writer, from 1995. I do not think that you want to see that. :smile:
PCX (RLE compression) and GIFs (LZW compression) were quickly replaced by the PNG format (which had better compression and was free) after Unysis decided to start charging to use the compression algorithm in the GIF format.
There are plenty of converters around (ImageMagick, Gwenview, Gimp) so maybe it is not worth spending too much time as it has been a long deprectated format.

I agree, I did not spend much time on updating that format anyway, so we should be good.