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Installation issue #131
Description
Hi,
Thanks a lot for developing this tool. I am looking to use it for some MERFISH data, but am experiencing issues re installation.
I am following the instructions from https://elihei2.github.io/segger_dev/installation/#installation-in-virtual-environment - I have my conda environment setup with python 3.11. After running:
git clone https://github.com/EliHei2/segger_dev.git
cd segger_dev
pip install -e ".[cuda12]"
When I try to then follow the initial steps in the dataset creation tutorial (https://elihei2.github.io/segger_dev/user_guide/data_creation/#xenium-with-optional-scrna-seq-derived-embeddings), I run into an error ModuleNotFoundError: No module named 'segger.data.sample' as soon as I run the command from segger.data.sample import STSampleParquet.
Digging a little deeper, it seems that in the segger repo I cloned, in each of the modules, when I look at the __init__.py files, they are empty?
Many thanks in advance.
Activity
Thienni-creator commentedon Feb 5, 2026
@andrewjkwok have you already tried with this?
from segger.data.parquet.sample import STSampleParquet because there is a sample.py script with the corresponding class in the parquet folder
EspressoKris commentedon Feb 6, 2026
Same issue, all tutorials lead to different versions and none work. Currently trying to install on a cuda12.2
EliHei2 commentedon Mar 7, 2026
hey! we are moving to the new version which is present on https://github.com/dpeerlab/segger, we're integrating everything into the new repo. thanks for your patience!
andrewjkwok commentedon Mar 9, 2026
Thanks. Looking at the new repo, the usage seems to be on the command line? Do the original usage instructions from https://elihei2.github.io/segger_dev/ still work, or should I simply wait for the new repo to be updated? Thanks again.
DininduSenanayake commentedon Mar 11, 2026
@EliHei2 Would it be possible for you to add a banner to https://github.com/EliHei2/segger_dev/blob/main/README.md informing researchers about the repository migration? . Thanks in advance