# \#getting-started **URL:** https://forum.allencell.org/tag/getting-started/8.md [Latest](https://forum.allencell.org/latest.md) · [Categories](https://forum.allencell.org/categories.md) · [Tags](https://forum.allencell.org/tags.md) --- ## [FNet setup issues due to outdated dependencies – any updated version or Docker?](https://forum.allencell.org/t/fnet-setup-issues-due-to-outdated-dependencies-any-updated-version-or-docker/792)
**Author:** [@ines\_varona](https://forum.allencell.org/u/ines_varona)\ **Replies:** 5\ **Last updated:** [March 25, 2026, 11:31pm UTC](https://forum.allencell.org/t/fnet-setup-issues-due-to-outdated-dependencies-any-updated-version-or-docker/792 "2026-03-25T23:31:18Z")
Hi everyone, I am currently running some experiments and would like to compare my results with outputs obtained using the FNet architecture. However, while setting up the environment and installing the required depende… --- ## [Thaw, expand and maintain MONO-ALLELIC mEGFP-TAGGED SOX2 cells in E8+ flex medium (Invitrogen) on Vitronectin-N coated wells](https://forum.allencell.org/t/thaw-expand-and-maintain-mono-allelic-megfp-tagged-sox2-cells-in-e8-flex-medium-invitrogen-on-vitronectin-n-coated-wells/771)
**Author:** [@leahpeng](https://forum.allencell.org/u/leahpeng)\ **Replies:** 1\ **Last updated:** [July 30, 2025, 8:09pm UTC](https://forum.allencell.org/t/thaw-expand-and-maintain-mono-allelic-megfp-tagged-sox2-cells-in-e8-flex-medium-invitrogen-on-vitronectin-n-coated-wells/771 "2025-07-30T20:09:44Z")
Hi, We would like to thaw, expand and maintain MONO-ALLELIC mEGFP-TAGGED SOX2 cells in E8+ flex medium (Invitrogen) on Vitronectin-N coated wells, which is different method comparing to the protocol provided by the Cori… --- ## [Found way around not well formed error and itkwidgets error, Classical Segmenter](https://forum.allencell.org/t/found-way-around-not-well-formed-error-and-itkwidgets-error-classical-segmenter/685)
**Author:** [@jcvance](https://forum.allencell.org/u/jcvance)\ **Replies:** 0\ **Last updated:** [March 8, 2024, 4:18pm UTC](https://forum.allencell.org/t/found-way-around-not-well-formed-error-and-itkwidgets-error-classical-segmenter/685 "2024-03-08T16:18:46Z")
Hi all, I was having an issue running demo\_TNNI1 on jupyter notebook for the classical segmenter. I am running it on Windows. When reading the TNNI1 data file, I got this note: “Failed to parse XML for the provided file… --- ## [AICSImage not Defined, Classical Segmenter](https://forum.allencell.org/t/aicsimage-not-defined-classical-segmenter/683)
**Author:** [@jcvance](https://forum.allencell.org/u/jcvance)\ **Replies:** 2\ **Last updated:** [February 27, 2024, 9:54pm UTC](https://forum.allencell.org/t/aicsimage-not-defined-classical-segmenter/683 "2024-02-27T21:54:07Z")
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\\1638… --- ## [Aicssegmentation not found in Jupyter, Classic Segmentation](https://forum.allencell.org/t/aicssegmentation-not-found-in-jupyter-classic-segmentation/681)
**Author:** [@jcvance](https://forum.allencell.org/u/jcvance)\ **Replies:** 3\ **Last updated:** [February 24, 2024, 12:11am UTC](https://forum.allencell.org/t/aicssegmentation-not-found-in-jupyter-classic-segmentation/681 "2024-02-24T00:11:31Z")
Hi, I am new to python and jupyter. I have been getting this error in demo\_TNNI1 on jupyter notebook: ModuleNotFoundError Traceback (most recent call last) ~\\AppData\\Local\\Temp\\ipykernel\_8960\\3994… --- ## [Downloading Cell Feature Data](https://forum.allencell.org/t/downloading-cell-feature-data/656)
**Author:** [@mtu2](https://forum.allencell.org/u/mtu2)\ **Replies:** 10\ **Last updated:** [September 8, 2023, 7:19pm UTC](https://forum.allencell.org/t/downloading-cell-feature-data/656 "2023-09-08T19:19:46Z")
Hi I’m new here and I am looking for cell morphology data such that I have a csv where each row is a cell and each column is a shape property(eg. area, perimeter). I don’t know exactly how to search for what I need on q… --- ## ["setup.py" not found error](https://forum.allencell.org/t/setup-py-not-found-error/354)
**Author:** [@AidanF](https://forum.allencell.org/u/AidanF)\ **Replies:** 1\ **Last updated:** [September 9, 2021, 5:18pm UTC](https://forum.allencell.org/t/setup-py-not-found-error/354 "2021-09-09T17:18:26Z")
Hi All, Getting the segmenter up and running on a new computer. No issues previously but running into this issue now when I issue the following command: "pip install -e .\[all\] ERROR: File “setup.py” not found. Director… --- ## [Cvapipeline\_analysis - Can I download a smaller dataset from Quilt to test the integrated modeling and analysis pipeline?](https://forum.allencell.org/t/cvapipeline-analysis-can-i-download-a-smaller-dataset-from-quilt-to-test-the-integrated-modeling-and-analysis-pipeline/278)
**Author:** [@MaryMirvis](https://forum.allencell.org/u/MaryMirvis)\ **Replies:** 5\ **Last updated:** [February 18, 2021, 12:05am UTC](https://forum.allencell.org/t/cvapipeline-analysis-can-i-download-a-smaller-dataset-from-quilt-to-test-the-integrated-modeling-and-analysis-pipeline/278 "2021-02-18T00:05:25Z")
Hello, I would like to follow the steps in cvapipeline\_analysis to better understand the integrated cell modeling and analysis workflow. However, cvapipe\_analysis loaddata run downloads 7.3 TB of data. I don’t have tha… --- ## [Getting started with forum basics](https://forum.allencell.org/t/getting-started-with-forum-basics/224)
**Author:** [@cells](https://forum.allencell.org/u/cells)\ **Replies:** 0\ **Last updated:** [July 9, 2020, 9:35pm UTC](https://forum.allencell.org/t/getting-started-with-forum-basics/224 "2020-07-09T21:35:41Z")
Getting Started As a first-time user, you may notice guides/alerts that popup as you begin to explore the forum site. These notes will automatically close after a short time, or you may close them manually. You can brows… --- ## [Quick Markdown guide for editing text in posts](https://forum.allencell.org/t/quick-markdown-guide-for-editing-text-in-posts/229)
**Author:** [@cells](https://forum.allencell.org/u/cells)\ **Replies:** 0\ **Last updated:** [July 20, 2020, 4:26am UTC](https://forum.allencell.org/t/quick-markdown-guide-for-editing-text-in-posts/229 "2020-07-20T04:26:52Z")
Some common markups: \*italic\* italic \*\*bold \*\* bold #Heading 1 Heading 1 ##Heading 2 Heading 2 \[Link\](link URL) Link \[Image|Size\](Image URL) \>block quote blockquote \* List - List List Horizon… --- ## [Forum Navigation](https://forum.allencell.org/t/forum-navigation/225)
**Author:** [@cells](https://forum.allencell.org/u/cells)\ **Replies:** 0\ **Last updated:** [July 9, 2020, 10:05pm UTC](https://forum.allencell.org/t/forum-navigation/225 "2020-07-09T22:05:32Z")
Home = Landing page = Latest update page You can always click on the Allen Cell Discussion Forum text link to get back to the Forum homepage. The “hamburger” menu An icon made of 3 horizontal lines is called a “ha… --- ## [Forum registration](https://forum.allencell.org/t/forum-registration/223)
**Author:** [@cells](https://forum.allencell.org/u/cells)\ **Replies:** 0\ **Last updated:** [July 7, 2020, 11:12pm UTC](https://forum.allencell.org/t/forum-registration/223 "2020-07-07T23:12:56Z")
Begin by clicking the teal \[Sign Up\] button in the right corner of the title banner seen on every forum webpage. The popup window gives you the option to sign up by creating a new account using your email. A… --- ## [The training images for the label free prediction](https://forum.allencell.org/t/the-training-images-for-the-label-free-prediction/237)
**Author:** [@Hanxix](https://forum.allencell.org/u/Hanxix)\ **Replies:** 1\ **Last updated:** [August 13, 2020, 9:22pm UTC](https://forum.allencell.org/t/the-training-images-for-the-label-free-prediction/237 "2020-08-13T21:22:56Z")
Hi, sorry for this maybe very basic question. I’m very new to image processing. I downloaded the label free tom20 images from the website: https://www.allencell.org/data-downloading.html#sectionLabelFreeTrainingData Wh… --- ## [Downloading LabelFree Image From Quilt](https://forum.allencell.org/t/downloading-labelfree-image-from-quilt/234)
**Author:** [@Hanxix](https://forum.allencell.org/u/Hanxix)\ **Replies:** 4\ **Last updated:** [August 10, 2020, 2:10pm UTC](https://forum.allencell.org/t/downloading-labelfree-image-from-quilt/234 "2020-08-10T14:10:17Z")
Hi, I would like to download the images from this page: https://open.quiltdata.com/b/allencell/packages/aics/label-free-imaging-collection I was able to browse the data manifest. If I would like to download part of th… --- ## [Error Loading Images in Look Up Table](https://forum.allencell.org/t/error-loading-images-in-look-up-table/231)
**Author:** [@AidanF](https://forum.allencell.org/u/AidanF)\ **Replies:** 6\ **Last updated:** [July 22, 2020, 11:32pm UTC](https://forum.allencell.org/t/error-loading-images-in-look-up-table/231 "2020-07-22T23:32:19Z")
Hi all, I’ve run into loading images in the look up table demo. Here’s the code: Loading the data FILE\_NAME = ‘\\Users\\Desktop\\AICSTest.tif’ reader = AICSImage(FILE\_NAME) IMG = reader.data.astype(np.float32) print(I…