Allen Cell Discussion Forum

Agave download problem

Hi,

I am having problems running AGAVE. I can dowload and open but it will crash the minute I try open an image. It also alerts my virus protection so possibly this is what is blocking it? Anyone else experience this/have a solution? I have tried on a few different PCs and laptops

Thanks!

Hi! Thanks for writing here. I’d like to help you get it up and running if we can!

It sounds like you are running on Windows?
Is there a logfile.log in the directory where the executable was unzipped? If so, that might provide some clues.

Currently AGAVE is very particular about which images it can open. It wants to be fed multichannel, single-time OME-TIFF files that have pixels stored as uint16. It can read some tiffs generated from imageJ as well, but they still need to be single-time and uint16.
(We are actively working to expand the possible file types from that starting point.)

There will be a fresh build soon that will stop crashing on files it doesn’t recognize and instead just log the error, so at least the program doesn’t stop working.

Just for reference, here is a downloadable example of a file that we expect to load in Agave:
https://files.allencell.org/api/2.0/file/download?collection=cellviewer-1-4&id=C70935
(You will have to unzip the file to extract the .ome.tiff file before loading in agave)

Thanks! I have I can load an image now if it is ome.tif format and work on it, although it is still freezing/crashing when using it. My image is very large, so possibly this is the issue.

Now that you have an image opening, the limiting factor is the image size and your system’s memory and speed (both cpu and gpu). It’s a very gpu intensive application. Currently agave will try to put the entire volume (up to 4 channels) in gpu memory. Depending on your needs, pre-downsampling the data can often still give good visualization results while making it small enough to fit in memory.