Open Microscopy Environment

Dear Melissa,

I read in the Release of OMERO & Bio-Formats 5.0.1 statement on the imageJ list that you had implemented

Adding image pyramid support for CellSens .vsi data

Is this accessible through BioFormat's macro language? If not, how can I access programmatically the different image resolutions contained within the VSI file?

Thank you as always for your time and your great work!

Oli

Hi Oli,

Is this accessible through BioFormat's macro language? If not, how can I access programmatically the different image resolutions contained within the VSI file?

The complete pyramid/resolution API is not exposed in Bio-Formats' macro commands for ImageJ, but you can access each resolution in the pyramid as an image series. Something like https://github.com/openmicroscopy/biofo ... tadata.txt would show the dimensions for all available resolutions. For .vsi datasets specifically, the last few image series will be thumbnails that aren't part of the pyramid; the remaining series will be sorted from largest (highest resolution) to smallest (lowest resolution).

We will consider better ways of exposing this functionality for 5.1.0.

Regards,
-Melissa

Dear Melissa,

Thank you for the excellent reply!

This new behavior is a bit troublesome as now we have duplication of the image series for the same data. Are there always a fixed number of images in the pyramid or is this dependent on other factors?

Also, asides from the first (max res) and last (lowest res) images, the intermediate resolution images are cropped/clipped, the missing pixels showing as black.

If you would like, I can send you a dataset showing this.

A better aproach, at least for us, was something that a previous version of BioFormats was doing. Adding the intermediate resolutions as separate slices or timepoints that we could manipulate by using crop on import. Though the fact that they are all the same (largest) size is not optimal, I can imagine.

Best

Oli

Hi Oli,

This new behavior is a bit troublesome as now we have duplication of the image series for the same data. Are there always a fixed number of images in the pyramid or is this dependent on other factors?

The number of resolution levels in the pyramid is generally dependent upon the size of the highest resolution.

Also, asides from the first (max res) and last (lowest res) images, the intermediate resolution images are cropped/clipped, the missing pixels showing as black.

If you would like, I can send you a dataset showing this.

We'd be happy to look into this if you can send an example. As usual, http://qa.openmicroscopy.org.uk/qa/upload is the best place to upload, but if you are uploading more than 2 GB of data let me know and I will send FTP instructions privately.

A better aproach, at least for us, was something that a previous version of BioFormats was doing. Adding the intermediate resolutions as separate slices or timepoints that we could manipulate by using crop on import. Though the fact that they are all the same (largest) size is not optimal, I can imagine.

We stopped using that approach because it quickly gets out of hand when there are also multiple Z sections and/or timepoints. The current approach is, from a modelling standpoint, much more correct. The Bio-Formats Java API allows for distinguishing between a series that is part of a pyramid and a series that is just extra data (see http://downloads.openmicroscopy.org/bio ... tionCount()); this just hasn't been mirrored in the macro language commands yet. It is our intention to do that no later than the 5.1.0 release.

Regards,
-Melissa

Dear Melissa,

We have the following problem:

- We uninstalled all the bioformats jars in Fiji to make sure only loci-tools.jar would provide us with the LOCI tools. We downloaded version 4.4.11, and tried with 4.4.10, 4.4.9 up to a week ago, we could still use our VSI reading macro properly, but since today we are hitting a bug: (With all versions).

What has changed? why did keeping a previous version of loci-tools.jar stop working? Do you have any info on this?

Just FYI, any version below 4.4.8 is no longer accessible from the bioformats website.

Best

Oli

Code: Select all

(Fiji Is Just) ImageJ 1.48v; Java 1.7.0_55 [64-bit]; Windows 7 6.1; 42MB of 22000MB (<1%)

java.lang.NoSuchFieldError: equalStrips
   at loci.formats.in.PyramidTiffReader.<init>(PyramidTiffReader.java:67)
   at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
   at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
   at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
   at java.lang.Class.newInstance(Class.java:374)
   at loci.formats.ImageReader.<init>(ImageReader.java:130)
   at loci.plugins.util.LociPrefs.makeImageReader(LociPrefs.java:82)
   at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:595)
   at loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:470)
   at loci.plugins.in.ImportProcess.execute(ImportProcess.java:140)
   at loci.plugins.in.Importer.showDialogs(Importer.java:125)
   at loci.plugins.in.Importer.run(Importer.java:77)
   at loci.plugins.LociImporter.run(LociImporter.java:79)
   at ij.IJ.runUserPlugIn(IJ.java:199)
   at ij.IJ.runPlugIn(IJ.java:163)
   at ij.Executer.runCommand(Executer.java:131)
   at ij.Executer.run(Executer.java:64)
   at java.lang.Thread.run(Thread.java:745)


To answer the question about the downloads, all past releases may be downloaded here: http://downloads.openmicroscopy.org/bio-formats/
I think there is an error on the main Bio-Formats page which has an outdated copy of the download page in addition to the current one, which I think you might have accessed (it has 4.4.8 on it). I've asked for this outdated link to be removed.


Thanks,
Roger

Hi Oli,

Can you clarify what url you were looking at that doesn't have the older Bio-Formats downloads? The page Roger is talking about shouldn't actually be publicly visible and I'd like to avoid anyone else coming across an out-of-date page.

Thanks very much,

Helen

Hi Helen,

The page I was accessing was
http://downloads.openmicroscopy.org/bio ... s/?C=M;O=D

For which the link was at the bottom of
http://downloads.openmicroscopy.org/bio-formats/5.0.2/

The links for the files in
http://downloads.openmicroscopy.org/bio-formats/4.4.8/
Are broken for example

I think anything before 4.4.8 is not working, as far as I checked.

Best

Oli

PS: The issue that needed us to use the old versions of Bioformats has been fixed on our side and we are now again happily keeping up with the great progress you guys are constantly making!

Hi Oli,

many thanks for the heads up. We added redirects our downloads page to fix broken links for the imagej plugin but these redirects indirectly caused the issue you rightfully reported.
Everything should be fixed now with all the old versions of Bio-Formats accessible and downloadable from http://downloads.openmicroscopy.org/bio-formats.

Sebastien

Hi Oli,

With respect to the error message that you are (were?) seeing, that indicates that you have multiple incompatible versions of Bio-Formats installed. Most likely, the Fiji updater installed some Bio-Formats 5.0.x jars which are conflicting with the 4.4.x version that you have installed by hand. If you still need to use 4.4.x, then going into the Fiji updater and removing all Bio-Formats jars with a 5.0.0, 5.0.1, or 5.0.2 version number should solve the problem (though that can cause problems with other plugins).

-Melissa