Bug 200 – Native support for the NIfTI stack format

Bug 200 - Native support for the NIfTI stack format


Summary:	Native support for the NIfTI stack format

Status:	RESOLVED FIXED

Product:	Fiji
Classification:	Unclassified
Component:	Plugins
Version:	unspecified
Hardware:	All Mac OS

Importance:	P2 normal
Assigned To:	Johannes Schindelin

URL:	http://nifti.nimh.nih.gov/

Depends on:
Blocks:

Reported:	2010-07-28 12:35 CDT by Charles Brossollet
Modified:	2012-04-20 22:35 CDT
CC List:	2 users (show)

See Also:

Description Charles Brossollet 2010-07-28 12:35:45 CDT

Fiji has support for the Analyze 7.5 format, by providing the Analyze_Reader plugin, but this format has been overcome by NIfTI-1. A plugin exists here: http://rsb.info.nih.gov/ij/plugins/nifti.html. It has also support for Analyze stacks, so it can replace the Analyze_Reader plugin. It would be great if Fiji was shipped with it.

Comment 1 Johannes Schindelin 2010-07-28 12:45:51 CDT

Do the files open using Plugins>LOCI>Bio-Formats Importer?

Comment 2 Charles Brossollet 2010-07-28 12:51:09 CDT

(In reply to comment #1)
> Do the files open using Plugins>LOCI>Bio-Formats Importer?
Yes, but it requires lot of mouse clicks to get them opened, and signed 16 bits data is interpreted as unsigned.

Comment 3 Johannes Schindelin 2010-07-28 12:55:34 CDT

In the long run, we might want to abolish the Analyze_Reader (and NIfTI) in favor of Bio-Formats, which provides a much more powerful way to read images: it outputs standardized data, and has a very good programmers' interface, unlike above-mentioned plugins.

So if there is a problem with the signed 16 bits format, it would be better to fix it in Bio-Formats, and then change Fiji such that the default reader for Analyze/NIfTI data is Bio-Formats (to avoid the many mouse clicks).

Would you care to upload a sample via Help>Upload Sample Image, please?

Comment 4 Charles Brossollet 2010-07-28 13:12:25 CDT

(In reply to comment #3)
That seems fine! uploaded file as "stack 16bits signed nifti.zip"

Comment 5 Curtis Rueden 2010-07-29 21:05:12 CDT

Dscho, please let us know if you need any help with the signed 16-bit issue.

Comment 6 Johannes Schindelin 2011-03-23 15:51:31 CDT

I just need more _time_! :-)

Comment 7 Melissa Linkert 2012-02-09 01:56:48 CST

For what it's worth, the uploaded sample dataset does open correctly using the latest version of Bio-Formats in the Fiji updater, cef7286.

Do note that the minimum and maximum pixel values in the image are 1 and 1905, respectively; as the autoscaling uses the actual min/max values and not the min/max values for the pixel type (-32768 and 32767 in this case), it's understandable how the image might "look" unsigned when the 'Autoscale' option is checked, since 1 is displayed as black instead of medium-grey.

Unchecking the 'Autoscale' option in the 'Bio-Formats Import Options' window results in a medium-grey image as expected (i.e. all of the pixels are in the middle of the intensity range for the pixel type), and checking the 'Display OME-XML metadata' option in the 'Bio-Formats Import Options' window and shows that the pixel type is indeed int16.

Comment 8 Johannes Schindelin 2012-04-20 22:35:45 CDT

Since it basically works with Bio-Formats, and since we want SCIFIO/Bio-Formats to be the long-term solution for the I/O problem, I think it is safe to close this ticket.