[Suggestion] qptifffile backend

[grenkoca]

Hey everyone! I also do low-level work with Phenocycler/CODEX data. I stumbled across your repository a while ago and found some of your methods really helpful for starting to work with this data. I found that .qptiff files were clunky to handle and lacked open-source support, so I wrote a streamlined extension of the tifffile library for qptiff files that might be useful https://github.com/grenkoca/qptifffile

The calls are inspired by openslide-python and is meant to help bridge the low-level image manipulation with conventional image analysis techniques. I'm open to any feedback or feature suggestions, but I hope it is helpful.

[grenkoca]

Oh, and here's an image.sc thread I wrote on it: https://forum.image.sc/t/qptifffile-python-bindings-for-easy-qptiff-file-manipulation-codex-phenocycler/112923. Sorry if this feels self-promotional-- I just think the data format is really promising, and hope that the open-source ecosystem keeps growing :)

TL;DR- install it with pip and enjoy easy file parsing and image manipulation:

In [1]: from qptifffile import QPTiffFile; import matplotlib.pyplot as plt

In [2]: f = QPTiffFile('../Phenocycler/Data/slides/Scan1.qptiff')

In [3]: f.read_region('DAPI')
Out[3]: 
memmap([[0, 0, 0, ..., 0, 0, 0],
        [0, 0, 0, ..., 0, 0, 0],
        [0, 0, 0, ..., 0, 0, 0],
        ...,
        [0, 0, 0, ..., 0, 0, 0],
        [0, 0, 0, ..., 0, 0, 0],
        [0, 0, 0, ..., 0, 0, 0]], dtype=uint8)

In [4]: img = f.read_region(
    ...:     layers=['DAPI'],
    ...:     shape=(500, 500),
    ...:     level=4)

In [5]: plt.imshow(img, cmap='gray')
Out[5]: <matplotlib.image.AxesImage at 0x12bcc8cb0>

In [6]: plt.show()

[kuang-da]

Hi @grenkoca, thanks for the comment, and I am glad you are interested in Aegle! We currently use open_as_zarr to open qptiff data with tifffile and transform it by zarr for subsetting and then write back as tiff with tifffile.

Seems your library gives a nice interface to explore the image in ipynb! Do you see it can be integrated into any part of Aegle?