Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment (particularly UW-Madison LOCI and Glencoe Software). Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
Yeepee! Thanks @joshmoore . I do not really understand the logic behind, but at least I can work with that.
Oki doki, I'll try the to use the main method first, which is public. I'll let you know how that goes ;-)
(That's what I did as well.) Good luck.
Aaah, just found out there's no pyramid option in this package. Is there a way to have a version with it ? It seems pyramid options are only in the develop branch...
Ah sorry there is... I have probably another problem is my function call. I'll dig
We need a shovel award, for people like @NicoKiaru. Every time you dig and report back your findings, you earn points. These go on your CV and employers take it more seriously than journal impact factor. </daydream>
Ahahah I need a shovel to hide right now. Just found out I forgot to remove a space in the ' -pyramid-scale' argument. I had to go full debug to find out this string is not equal to '-pyramid-scale'.
Hi! Is there a way to check in advance whether making a new memo file will be needed or not ? This could be a useful information to give to users. HCS dataset can take a few minutes to open when a memo file has to be re-created.
Hey @NicoKiaru. I don't think so. Just asking the others now.
The update notes say as much, but that's not overly useful.
I'm pretty sure it's a runtime issue down inside of Kryo
Melissa adds that there's a skipSave method which you could set, so when kryo throws an exception loadMemo will return null. On the next opening, then you'd want/need to save.
We have some 1-5TB data files in nd2 format, and I would like to convert them to something the bigdataviewer can manage. I suppose an h5 file with associated xml.
@odinsbane I might be wrong (my memory is not the best about it), but I believe you need to open the .nd2 right away with BDV - it will use Bio-Formats under the hood and create the appropriate .h5 file for you.