Unable to download Allen Mice Atlas

[LeoJuh]

When I press the first "Download" button everything works, but when I press the "Download Meshes" button, the third bar is stuck at 0% and never changes.

[JingyiGF]

May I know which version of HERBS are you using? I wonder if you click the 'download mesh' button before the atlas data finished downloading?

[LeoJuh]

Hello again!

I am using the 0.0.14 version.

I waited until the above two green bars had reached 100% and then pressed the "download mesh" button, so I don´t think that explains the problem unfortunately. I tested this on two different computers and faced the same issue on both.

[bigbrainmay]

Hello! I am having the same issue with downloading the Allen Mice Atlas. I followed the recommendations on the October 5, 2022 thread regarding this same issue (waited until atlas data finished downloading, waited until all 671 mesh files were downloaded before processing), but when I click "Process," "Please wait until finishing downloading files" appears; as far as I know, all the necessary files have been downloaded. I did wait several hours to see if anything else would download, but I didn't notice any new files. Any advice would be appreciated!

[AthiemoneZero]

Hello! I also have the same issue. I wonder if there is a way to download and process allen atlas manually. Thanks a lot for any advice!

[HDClark94]

Hi, I'm also having the same issue!

[JingyiGF]

Hi all, sorry for the late reply and thanks for updating and reporting the issue. I am currently a bit busy but I will have a look during the coming weekend. Will update you afterwards. One thing would like to check, are you all using Windows 10? Many thanks!

[AthiemoneZero]

Hi all, sorry for the late reply and thanks for updating and reporting the issue. I am currently a bit busy but I will have a look during the coming weekend. Will update you afterwards. One thing would like to check, are you all using Windows 10? Many thanks!

Very thank you for your timing reply. I do use window10 system. Luckily and unexpectedly I solved this problem after I re-installed my conda env. This time I restricted python version == 3.9.0 in a new conda env and used pip to install HERBS (I run anaconda prompt in pycharm terminal). After that I strictly follow instruction in the CookBook (never press any button till it finish downloading Allen Mice Atlas).

It cost a little time in downloading mouse atlas(10um) under my network situation and cost more on meshes download. But this time it went so smooth as I noticed the process bar of downloading meshes was running, which might represent it worked normally. And then I still followed instrution to process downloaded atlas and meshes. It cost more time but I always can find that the process bar keep going on. Hope this description can help you.

by the way, I intergrated import herbs and herbs.run_herbs() into a python file and run it in terminal. It work well now although I have no idea how I fixed this bug

[JingyiGF]

HI @AthiemoneZero, thank you so much for the update! which version of python did you use before? I would like to test on the same version :-)

[HDClark94]

I am using Windows 11 with conda installed python 3.8. I attempted again with python 3.9 and the atlas installed just fine.

[JingyiGF]

HI, I just tested python 3.8.10 on Windows 10 with conda env in VScode. Downloading atlas is smooth, but it did take me 4 mins until the meshes started after the atlas finished. In total, downloading Allen 10um took me less than 20 mins under my network situation. The problem so far I have faced : Python version lower than 3.8.10 will not work, and while downloading, other buttons can be clicked to avoid signal conflicts. Let me know if there is other problems.

Thanks again for the updates :-)

[AthiemoneZero]

HI @AthiemoneZero, thank you so much for the update! which version of python did you use before? I would like to test on the same version :-)

sorry for late reply. I used to install python via conda install. It should be latest version of python and it is 3.10.9

[chris-angeloni]

Can also confirm that for some reason using a conda environment with Python 3.9 solves this issue on Windows 10.

conda create -n 'herbs' python=3.9.0, then conda activate herbs, then pip install herbs

[Aexolowski]

Hey all, just FYI we had the same issue with python 3.10.9 and it seems that the mesh download really only works with 3.9.2.

[vasilisazhukova]

Hi all, I have the same problem despite I have python 3.11.7. I tried to download atlases with 10 and 50 microns.