Hi,
I would like to run CAFI using my local resources. Would you mind sharing a requirement text file that includes all the dependencies and packages necessary to run CAFI on a local conda environment? Thanks!

Hi,
I tried to run the ZoomingSlowMo_4_Microscopy.ipynb notebook with mine own and also provided datasets, however it throwed following error in section 4.3.1 with both datasets:
RuntimeError: cuda runtime error (77) : an illegal memory access was encountered at /pytorch/aten/src/THC/THCCachingHostAllocator.cpp:296

In another case, I was trying to use a 5D dataset (TZXYC). When I give the file in section 3 it gives following result: "The TIF image dimensions are (20, 19, 2, 1024, 1024)". I guess it was supposed to give the image dimensions as (20, 19, 1024, 1024, 2). Probably because of this it couldn't prepare the data for training. Then I splitted channels and reached until section 4.3.1.
Please let me know if you need further information.
I am interested to use the notebook for Airyscan live cell imaging data which are of between 20-50 timepoints, around 20 z-slices and less than 1024x1024 in dimensions.

I appreciate your quick response.

Regards,
Sujan

Hello and first off, thank you for making your work publicly available !

I have been trying to run the ZoomingSlowMo Colab but Google Colab removed support for Tensorflow 1, and it is not possible to use %tensorflow_version 1.x magic anymore.
I've tried to make it work with Tensorflow 2.x but keep getting during the requirement installation step.
Is there by any chance an up-to-date version of the Colab available ?
Thank you for your answer :)

I am trying to follow the DAIN_4_Mic notebook by running it on collab with GPU enabled and after those first lines:

import os

!wget -c https://repo.anaconda.com/miniconda/Miniconda3-4.5.4-Linux-x86_64.sh
!chmod +x Miniconda3-4.5.4-Linux-x86_64.sh
!bash ./Miniconda3-4.5.4-Linux-x86_64.sh -b -f -p /usr/local

I get this error:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Traceback (most recent call last):
  File "/usr/local/bin/conda", line 7, in <module>
    from conda.cli import main
ModuleNotFoundError: No module named 'conda'
Traceback (most recent call last):
  File "/usr/local/bin/conda", line 7, in <module>
    from conda.cli import main
ModuleNotFoundError: No module named 'conda'

Thanks for the help.

Hi!

I got the following error while installing DAIN_4_Microscopy.ipynb notebook:

---------------------------------------------------------------------------

ModuleNotFoundError                       Traceback (most recent call last)

<ipython-input-3-09fd65144275> in <module>()
     52 _ = (sys.path.append("/usr/local/lib/python3.6/site-packages"))
     53 sys.path.insert(0,'/content/DAIN/load_functions')
---> 54 from download_from_gdrive import download_file_from_google_drive
     55 best_pretrained = "1EYgrdsaffVJuQlcBSK4dGqO2BXBkSlZf"
     56 if not os.path.exists("/content/DAIN/model_weights"):

ModuleNotFoundError: No module named 'download_from_gdrive'

Solved it with:

!pip install googledrivedownloader
from google_drive_downloader import GoogleDriveDownloader as gdd
gdd.download_file_from_google_drive(best_pretrained, file_path)

When I run the step of: 2. Compile the DCNv2:

cd $ZOOMING_ROOT/codes/models/modules/DCNv2
bash make.sh         # build

It says .../CAFI-main/ZS4Mic/Zooming-Slow-Mo-CVPR-2020/codes/models/modules/DCNv2/src/cuda/dcn_v2_cuda.cu:7:10: fatal error: THC/THC.h: 没有那个文件或目录
    7 | #include <THC/THC.h>
      |          ^~~~~~~~~~~
compilation terminated.