AICSImage not Defined, Classical Segmenter

Software & Code
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1

Hi all,

I am having difficulty running playground_npm1. After loading the image, I get this error:

NameError Traceback (most recent call last)
~\AppData\Local\Temp\ipykernel_28628\1638661765.py in
1 FILE_NAME = ‘D:\Classic_segmenter\aics-segmentation\demo_data\RAB5_demo_data.tif’
----> 2 reader = AICSImage(FILE_NAME)
3 IMG = reader.data.astype(np.float32)
4
5 print(IMG.shape)

NameError: name ‘AICSImage’ is not defined

I installed the segmenter earlier today on Windows with no issues. In this playground, AICSImage is part of aicsimageio. Do you know what is causing the problem and how to fix it?

Thank you so much,
Julia Vance

2

Hi @jcvance,
Sorry you’re running into this issue! Does the first cell (importing aicsimageio and the core algorithm functions) run without errors? What version of aicsimageio do you have (can be seen with ! pip show aicsimageio in the jupyter notebook.

  • Benji
3

Hi Benji,

I have version 4.7.0 . I had followed the instructions from this page (aics-segmentation/docs/installation_windows.md at main · AllenCell/aics-segmentation · GitHub). Is this the right place or is there a more updated area that I am missing?

Thank you so much,
Julia