Is there any need to add a tifffile library as a dedicated tifreader?

[JavaZeroo]

I have tested that reading a large file with PIL takes about 4 times longer than tifffile. 🤯

If possible, I can submit a PR for tif_reader based on tifffile. 🤩

In addition, I wonder why WSIReader was removed, it looks like he has been implemented to read tif files using tifffile. 🤔

Speed Test

[KumoLiu]

Hi @JavaZeroo, thanks for your interest here.
We didn't remove WSIReader, just put it under monai/data folder, and it still support tifffile backend.

MONAI/monai/data/wsi_reader.py

Line 475 in 9c97777

supported_backends = ["cucim", "openslide", "tifffile"]

Thanks!

[JavaZeroo]

Thanks! Thats really help a lot! ❤️

[JavaZeroo]

How to open single channel tif image? Im using TiffFileWSIReader

transforms.LoadImaged(keys=["image"], reader="TiffFileWSIReader", mode='r+' ),

I tried mode='r+' to avoid channel check, but it is doesn't work. :(

https://github.com/Project-MONAI/MONAI/blob/9c9777751ab4f96e059a6597b9aa7ac6e7ca3b92/monai/data/wsi_reader.py#LL1179C1-L1186C30

[KumoLiu]

Hi @JavaZeroo, could you please share one data then I can take a look at the error?

[JavaZeroo]

00.tif.zip

[JavaZeroo]

Which is from Kaggle