Hi Sasha,, I am working with CZI files too and could share some experience. I am using Christophs czifile package with parallel processing and it works great. I highly recommend not to convert the CZI files because it will become a nightmare (we did that before) and you will loose many information's (e.g. region ID, polygon points...). I can share some code if you like. Unfortunately I am using OpenCV for image processing because it's much faster compared to scikit-image and we have a large amount of data (200 GB per run). Cheers Stefanie Am Fr., 25. Okt. 2019 um 02:38 Uhr schrieb Cedric Espenel < cedric.espenel@gmail.com>:
Hi Sasha,
Did you try PIMS bioformats for you data?
http://soft-matter.github.io/pims/v0.4.1/bioformats.html
Best,
Cedric
On Thu, Oct 24, 2019 at 5:28 PM Augusto Kielbowicz <augusto.kiel@gmail.com> wrote:
Hi,
I just started a new project analyzing some images that are in czi format and looking around there is not much support for them. I found that there is a czifile package in which there is a function to transform the file into a memory mappable tiff file. This comes very handy given that the images are big enough (~7gb) to cause trouble being in memory, but it's not working perfectly for me.
I wanted to know what it's the common way to work with this kind of large images. It's normal to convert it to TIFF and work with that? Or is there a better format to work with?
It's my first time working with image data and files this big so I'm learning a lot, it's being great and I'm loving all the cool stuff that skimage can do. Now I'm starting to look into dask-image and it seems promising.
Thank you, Sasha _______________________________________________ scikit-image mailing list -- scikit-image@python.org To unsubscribe send an email to scikit-image-leave@python.org
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