Open segmented*.AIM with Fiji or Bio-Formats for Matlab

[auzehong]

I can open raw/unprocessed Scanco *.AIM files with Fiji and Bio-Formats for Matlab, but a *.AIM that has been processed/segmented with Scanco Image Processing Language (Scanco IPL) yields errors and fails to open in Fiji and Bio-Formats for Matlab. As far as I am concerned, the processed/segmented *.AIM contains more metadata in its file header than raw/unprocessed ones. Is there any way to overcome this problem so the processed/segmented *.AIM can be opened to extract the *.TIFF sequence?

The processed and unprocessed *.AIM files are uploaded to http://qa.openmicroscopy.org.uk/qa/feedback/10913/.

[sbesson]

Hi,

thanks for uploading these sample files. I can reproduce the error both with the Bio-Formats 5.0.8 and the HEAD of the development line. The unprocessed AIM opens without error while the segmented AIM throws an exception at opening time.

Before opening a ticket to address this issue, you mentioned that the processed aim file is expected to contain much more metadata. On the sample files you uploaded, the raw data file size is 40M while the processed data file is 2.2M. Do you know if the processed file is also meant to contain the initial raw data or does it work in coordination with another file (like the raw data file)?

Best,
Sebastien

[sanchi4u]

Hi,

I am not sure to what extent this issue was resolved. As for me, the .AIM file opens perfectly, I can view each image in the stack by scrolling through them. However, when I open a segmented AIM file, it alters the number of slices in the stack and each slice shows duplicates of the image. I am not sure if this issue is because there isn't a proper reader for segmented AIM files or this needs some pre-processing before importing through bio-formats.

All my files have 168 slices, however, for seg AIM, only 84 slices can be seen. Any help is resolving this issue is much appreciated.

I have uploaded a screenshot of the issue and a sample segmented file here.

http://qa.openmicroscopy.org.uk/qa/feedback/17384/
http://qa.openmicroscopy.org.uk/qa/feedback/17385/

Thanks!!

[sbesson]

Hi,

thanks for uploading your sample files. Using the latest version of Bio-Formats (5.2.3) in Fiji, I was unable to reproduce your issue though as the file opens as a 168 slices images for me.

Which version of Bio-Formats are you using (Help > About Plugins > Bio-Formats Plugins) and on which operating system?

Best,
Sebastien

[sanchi4u]

Hi Sebastien,

Thank you for your response. I am using Bio-formats 5.2.3 in Fiji and it's running on MacOS X Yosemite 10.10.5.

In this case it is showing 168 slices but the last few slices are empty. Also are you not getting duplicate images in each slice?

Could this be because of the settings for Bio-formats import options page? Attached below is the settings that I am using.

Thanks,
Sanchita

Bio-formats import.png (155.89 KiB) Viewed 3402 times

[sbesson]

Hi,

thanks for the information. You are correct that the image opens as 168 z-slices but half of them are empty.

The importer options should be irrelevant. At the moment, segmented AIM images are opened exactly like regular AIM images but this assumption might not hold and segmented images might require some special logic. Unfortunately we do not have access either to a specification for the AIM file format or to a software that establishes the ground truth of how to read these images.

In the meantime, I can open either a ticket to record this issue and cc you on it if you are interested.

Best,
Sebastien