ahnlabb
Support for SlideBook6
Just noticed that I did this a while ago and never got around to open a PR. The code has changed since then, so maybe some of these changes are no longer necessary.
I should also add that I don't have an immediate need for it anymore, but hopefully this will be of help to someone else.
Thank you for taking the time to open this PR! Like you're saying some things have changed and it looks like the issues in bf_import and read_stack that you're addressing here have been taken care of since then.
As far as I can tell from the Bio-Formats documentation there is some basic support for SlideBook (formats/3i SlideBook) in vanilla BF. Do you remember what your experience was like without using the SlideBook6Reader.jar? Do you know of any public datasets of the sorts of files you were trying?
I'm hesitant to add a second jar without adding better error messages for users when the download has failed in the build step somehow. I guess that's really something we would need anyways so I'll add an issue for it.
Using one buffer to load the slices like you attempted is an interesting idea! Did you ever figure out why that didn't work?
As far as I can tell from the Bio-Formats documentation there is some basic support for SlideBook (formats/3i SlideBook) in vanilla BF. Do you remember what your experience was like without using the SlideBook6Reader.jar?
I recall it not working at all for the files I had at hand back then. This was for a class project and I have since then garbage collected all memory I have of this.
I'm hesitant to add a second jar without adding better error messages for users when the download has failed in the build step somehow. I guess that's really something we would need anyways so I'll add an issue for it.
Maybe use artifacts instead of manually downloading?
Using one buffer to load the slices like you attempted is an interesting idea! Did you ever figure out why that didn't work?
I recall running out of memory a lot, but I don't recall why that particular call doesn't work.
Do you know of any public datasets of the sorts of files you were trying?
No, they files I was given were from ongoing research. One could maybe ask https://zenodo.org/record/4034929#.X5XSNccpB-E if they would mind creating a SlideBook6 file of their training set.