ome
Feature request: Disable thumbnails in BF plugin
This is a request which was received via https://forum.image.sc/t/bio-formats-xml-hdf5-reader-performance/30458
When using the Bio-Formats plugin in FIJI it would be useful to provide the option to disable thumbnail generation in order to improve performance at the Series select window.
This issue has been mentioned on Image.sc Forum. There might be relevant details there:
https://forum.image.sc/t/bio-formats-xml-hdf5-reader-performance/30458/4
Another request for this feature has been received in forum thread: https://forum.image.sc/t/speeding-up-metamorph-file-reading-with-bioformats/42532/17
From the thread:
For metamorph file I have a time lapse of 179 time points and 128 positions, each time point is a separate stk file with 3 Z-slices a 28 MB. All in all over 22000 files. Just the opening of the series choice menu takes between 1 and 2 hour.
This issue has been mentioned on Image.sc Forum. There might be relevant details there:
https://forum.image.sc/t/speeding-up-metamorph-file-reading-with-bioformats/42532/19
Hello, are there any news on implementing a nopix opening in bioformat? Generally improving the reading in of multi-file data?
Currently metamorph 18720 images (multi-position+time-lapse in total 294 GB) takes several hours until one gets the first response of bioformat in Fiji. I basically gave up. Currently I am reading each position as image-sequence and this is truly not the right choice.
Using the command line tool, reading of the information with the non-pix option is done within 15 minutes (which honestly is still quite long).
I guess this is also a problem for OMERO as it can't load this kind of data in an efficient way.
Crossposting from the ImageSC thread:
Using the Memoizer through a macro or plugin is likely the best solution here. Yes in the long term it would be good if this functionality was available in the plugin but the reality right now is that there is no funding or resource availble for developing new plugin features. As an open source project I would certainly welcome community contributions if anyone has the time and ability to make progress on this or any other plugin related imporvments.
To create an ImagePlus using the Memoizer I would suggest using code similar to bioformats/Read_Image.java at develop · ome/bioformats · GitHub, except when creating the reader at bioformats/Read_Image.java at develop · ome/bioformats · GitHub you should be able to additionally wrap it with Memoizer as well as ChannelSeperator. This will still be slow for the first read but should hopefully improve the speed greatly for any subsequent reads.