# Segmenter **URL:** https://forum.allencell.org/c/software-code/segmenter/16.md [Latest](https://forum.allencell.org/latest.md) · [Categories](https://forum.allencell.org/categories.md) · [Tags](https://forum.allencell.org/tags.md) --- ## [About the Segmenter category](https://forum.allencell.org/t/about-the-segmenter-category/254)
**Author:** [@cells](https://forum.allencell.org/u/cells)\ **Replies:** 0
\*Notice: Please start new topics/posts on image.sc forum for Segmenter since we have joined them as a community partner! This category is now closed. The Allen Cell & Structure Segmenter is a Python-based open source to… --- ## [3D single cell image data set](https://forum.allencell.org/t/3d-single-cell-image-data-set/357)
**Author:** [@RexH](https://forum.allencell.org/u/RexH)\ **Replies:** 12\ **Last updated:** [October 27, 2021, 10:02pm UTC](https://forum.allencell.org/t/3d-single-cell-image-data-set/357 "2021-10-27T22:02:58Z")
Hello Allen Cell Segmentation Developers, I have read “Robust integrated intracellular organization of the human iPS cell” and “The Allen Cell and Structure Segmenter”. I am trying to create a 3D single cell image data … --- ## ["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… --- ## [Iterative Deep Learning Workflow](https://forum.allencell.org/t/iterative-deep-learning-workflow/340)
**Author:** [@RexH](https://forum.allencell.org/u/RexH)\ **Replies:** 10\ **Last updated:** [August 20, 2021, 7:02pm UTC](https://forum.allencell.org/t/iterative-deep-learning-workflow/340 "2021-08-20T19:02:19Z")
Hello Allen Segmentation Developers, I am trying to use the Iterative Deep Learning Workflow on a Windows 10 operating system utilizing a Bash Shell with an Ubuntu command window (Windows Subsystem for Linux) (version 1… --- ## [Playground 9: Segmentation workflows for lamin b1 (interphase)](https://forum.allencell.org/t/playground-9-segmentation-workflows-for-lamin-b1-interphase/320)
**Author:** [@antho](https://forum.allencell.org/u/antho)\ **Replies:** 13\ **Last updated:** [June 9, 2021, 9:33pm UTC](https://forum.allencell.org/t/playground-9-segmentation-workflows-for-lamin-b1-interphase/320 "2021-06-09T21:33:24Z")
Hi, I have installed aics-segmentation and the machine learning section too, everything works great so far. I have a question regarding the segmentation for laminb1 workflow : It is design to work with 3d images (z … --- ## [Segmentation error after windows update](https://forum.allencell.org/t/segmentation-error-after-windows-update/316)
**Author:** [@Raynor97](https://forum.allencell.org/u/Raynor97)\ **Replies:** 4\ **Last updated:** [April 29, 2021, 7:25pm UTC](https://forum.allencell.org/t/segmentation-error-after-windows-update/316 "2021-04-29T19:25:11Z")
I’m using aics-segmentation/lookup\_table\_demo/playground\_filament3d.ipynb. However, after the recent windows update, the code cannot work as before. Attached is the error code. I tried reinstall the aics-segmentation bu… --- ## [3D image analysis after classic segmentation](https://forum.allencell.org/t/3d-image-analysis-after-classic-segmentation/304)
**Author:** [@ashapeng](https://forum.allencell.org/u/ashapeng)\ **Replies:** 2\ **Last updated:** [March 23, 2021, 6:29pm UTC](https://forum.allencell.org/t/3d-image-analysis-after-classic-segmentation/304 "2021-03-23T18:29:07Z")
Hi everyone, I am new to aics-segmentation. I have two questions about the classic segmentation pipepline. How to avoid the over-segementation. like the image shown below, signals in top and bottle layers seem to be p… --- ## [Nucleus DAPI segmentation (only)](https://forum.allencell.org/t/nucleus-dapi-segmentation-only/289)
**Author:** [@antho](https://forum.allencell.org/u/antho)\ **Replies:** 8\ **Last updated:** [February 25, 2021, 3:09pm UTC](https://forum.allencell.org/t/nucleus-dapi-segmentation-only/289 "2021-02-25T15:09:47Z")
Hi, I found the workflows that you share very nicely on your website. I would like to do segmentation on cells (3d and 2d) mainly to segment the nucleus (DAPI), FISH signal (3d), 3d dots and membranes. Looking at the … --- ## [Image size error- Same image has different sizes on different cpus?](https://forum.allencell.org/t/image-size-error-same-image-has-different-sizes-on-different-cpus/275)
**Author:** [@mramsahoye](https://forum.allencell.org/u/mramsahoye)\ **Replies:** 7\ **Last updated:** [February 15, 2021, 9:39pm UTC](https://forum.allencell.org/t/image-size-error-same-image-has-different-sizes-on-different-cpus/275 "2021-02-15T21:39:52Z")
Hello! So I have Allen Segmenter downloaded on my laptop and on a desktop…but for some reason the desktop is having issues opening files because of the following error: I noticed in the “Loading the Data” part of the … --- ## [No module named 'aicssegmentation'](https://forum.allencell.org/t/no-module-named-aicssegmentation/274)
**Author:** [@FutureCScientist](https://forum.allencell.org/u/FutureCScientist)\ **Replies:** 7\ **Last updated:** [December 22, 2020, 9:55pm UTC](https://forum.allencell.org/t/no-module-named-aicssegmentation/274 "2020-12-22T21:55:20Z")
Hi Mr/Ms I am new into using the Allen Cell Structure, I had problems during the installation of “pip install -e .\[all\]”. I tried to dig in what could be the problem, also tried to find a solution. I ran the command p… --- ## [Image dimensions seem to be assigned incorrectly by aicsimageio when running deep learning segmenter](https://forum.allencell.org/t/image-dimensions-seem-to-be-assigned-incorrectly-by-aicsimageio-when-running-deep-learning-segmenter/271)
**Author:** [@lynn](https://forum.allencell.org/u/lynn)\ **Replies:** 12\ **Last updated:** [December 22, 2020, 7:30am UTC](https://forum.allencell.org/t/image-dimensions-seem-to-be-assigned-incorrectly-by-aicsimageio-when-running-deep-learning-segmenter/271 "2020-12-22T07:30:20Z")
I’ve been trying to figure out this issue for a while and I’ve gotten pretty stumped, so I figured I would ask here to see if anyone can help. I have a feeling the fix isn’t that hard, I’m just not very experienced deali… --- ## [Batch Processing Error](https://forum.allencell.org/t/batch-processing-error/217)
**Author:** [@Leo\_Mv](https://forum.allencell.org/u/Leo_Mv)\ **Replies:** 9\ **Last updated:** [November 21, 2020, 8:13pm UTC](https://forum.allencell.org/t/batch-processing-error/217 "2020-11-21T20:13:03Z")
Hi, I am trying to batch process my images in the segmenter using the provided template and tutorial. I have followed all the instructions, however, when I try to execute the process I keep getting an error (see attache… --- ## [Opening segmentation .py files in python](https://forum.allencell.org/t/opening-segmentation-py-files-in-python/248)
**Author:** [@AidanF](https://forum.allencell.org/u/AidanF)\ **Replies:** 7\ **Last updated:** [October 27, 2020, 5:30pm UTC](https://forum.allencell.org/t/opening-segmentation-py-files-in-python/248 "2020-10-27T17:30:24Z")
Hi all, I’ve successfully been running the segmentation through the jupyter notebooks for individual image files. I now am attempting to loop files through the .py files in either the anaconda prompt (anaconda 3) or py… --- ## [Errors with running the demo of the Classic Image Segmentation](https://forum.allencell.org/t/errors-with-running-the-demo-of-the-classic-image-segmentation/207)
**Author:** [@mramsahoye](https://forum.allencell.org/u/mramsahoye)\ **Replies:** 17\ **Last updated:** [September 28, 2020, 9:25pm UTC](https://forum.allencell.org/t/errors-with-running-the-demo-of-the-classic-image-segmentation/207 "2020-09-28T21:25:19Z")
Hello! I’ve been having some issues with the classic image segmentation demos. No matter which of the three kernels I have that are currently available to me, I cannot get it to run because the libraries are not downloa… --- ## [Using deep learning segmenter to segment whole cells](https://forum.allencell.org/t/using-deep-learning-segmenter-to-segment-whole-cells/246)
**Author:** [@lynn](https://forum.allencell.org/u/lynn)\ **Replies:** 3\ **Last updated:** [September 3, 2020, 2:28am UTC](https://forum.allencell.org/t/using-deep-learning-segmenter-to-segment-whole-cells/246 "2020-09-03T02:28:37Z")
I’ve been exploring using the deep learning segmenter to segment whole cells that express a membrane-GFP label. It worked much better than I expected considering the segmentation workflow I used to generate training data… --- ## [Lamin B1 Segmentation](https://forum.allencell.org/t/lamin-b1-segmentation/247)
**Author:** [@pushkar](https://forum.allencell.org/u/pushkar)\ **Replies:** 1\ **Last updated:** [August 30, 2020, 2:31am UTC](https://forum.allencell.org/t/lamin-b1-segmentation/247 "2020-08-30T02:31:41Z")
Hi, I am trying to segment Lamin B1 channel. I followed the AICS laminB1 notebook. The cross sections seem decent quality but I am unable to get the top and bottom layers like shown in the example in this page. What ca… --- ## [Changing the code of playground\_filament3D to support a 2D image](https://forum.allencell.org/t/changing-the-code-of-playground-filament3d-to-support-a-2d-image/239)
**Author:** [@cmartin98](https://forum.allencell.org/u/cmartin98)\ **Replies:** 1\ **Last updated:** [August 13, 2020, 9:23pm UTC](https://forum.allencell.org/t/changing-the-code-of-playground-filament3d-to-support-a-2d-image/239 "2020-08-13T21:23:18Z")
Specifically, we’re trying to segment images of epithelial cells with an E-cadherin fluorescent label, so we sought to try the filament playground. However, our images are 2D and it looks like this script only works for … --- ## [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… --- ## [Error when running Look Up Table Demo Classic Image Segmentation](https://forum.allencell.org/t/error-when-running-look-up-table-demo-classic-image-segmentation/227)
**Author:** [@AidanF](https://forum.allencell.org/u/AidanF)\ **Replies:** 6\ **Last updated:** [July 21, 2020, 2:05pm UTC](https://forum.allencell.org/t/error-when-running-look-up-table-demo-classic-image-segmentation/227 "2020-07-21T14:05:32Z")
Hi all, Very new to coding, and attempting to install and run the Allen Classic Image Segmentation. The installation went smooth until the very last step, Step 3.3 Test Segmenter. Here is the error I get: (segmentation… --- ## [Filling empty pixels in 3D segmentation](https://forum.allencell.org/t/filling-empty-pixels-in-3d-segmentation/191)
**Author:** [@pushkar](https://forum.allencell.org/u/pushkar)\ **Replies:** 1\ **Last updated:** [May 13, 2020, 4:26pm UTC](https://forum.allencell.org/t/filling-empty-pixels-in-3d-segmentation/191 "2020-05-13T16:26:37Z")
Hi, I am currently trying perform 3D segmentation on cells using beta actin channel. One issue I am facing is that the walls appear to be ‘porous’ - i.e. there are holes in the wall that connect the cells. This makes it… --- ## [Batch processing for segmenter tool](https://forum.allencell.org/t/batch-processing-for-segmenter-tool/143)
**Author:** [@amycaitriona](https://forum.allencell.org/u/amycaitriona)\ **Replies:** 8\ **Last updated:** [May 13, 2020, 4:05pm UTC](https://forum.allencell.org/t/batch-processing-for-segmenter-tool/143 "2020-05-13T16:05:36Z")
I am using your segmenter tool and it is working quite well so far, I was just wondering if there was an option for batch processing? Thanks! --- ## [Writing to a TIFF File with Voxel Spacing \[Error in Codebase\]](https://forum.allencell.org/t/writing-to-a-tiff-file-with-voxel-spacing-error-in-codebase/184)
**Author:** [@dylanmendonca](https://forum.allencell.org/u/dylanmendonca)\ **Replies:** 6\ **Last updated:** [March 6, 2020, 8:27pm UTC](https://forum.allencell.org/t/writing-to-a-tiff-file-with-voxel-spacing-error-in-codebase/184 "2020-03-06T20:27:17Z")
I noticed a few things. The metadata for my image does not come from the TIFF file even after using AICSImage. Also, how do I specify the metadata in the exported tiff file. I was digging through your code base and noti… --- ## [Classic Image Segmentation installation](https://forum.allencell.org/t/classic-image-segmentation-installation/177)
**Author:** [@tdaugird](https://forum.allencell.org/u/tdaugird)\ **Replies:** 9\ **Last updated:** [February 12, 2020, 10:08pm UTC](https://forum.allencell.org/t/classic-image-segmentation-installation/177 "2020-02-12T22:08:15Z")
I am running into a bit of a snag when I try to install the Classic Image Segmentation Workflow. During installation, when i try run: pip install -e .\[all\] in anaconda prompt I get the following error: ERROR: Command… --- ## [Dilation function speed](https://forum.allencell.org/t/dilation-function-speed/168)
**Author:** [@pushkar](https://forum.allencell.org/u/pushkar)\ **Replies:** 5\ **Last updated:** [January 31, 2020, 12:12am UTC](https://forum.allencell.org/t/dilation-function-speed/168 "2020-01-31T00:12:40Z")
I noticed that the dilation function used in segmenting particles appears to take ~2 hours even though it says 2-3 minutes in the notebook. I have about 2000- 5000 ‘particles’ in my zstack. I wasn’t able to test the tu… --- ## [Separating zstacks into individual cells](https://forum.allencell.org/t/separating-zstacks-into-individual-cells/167)
**Author:** [@pushkar](https://forum.allencell.org/u/pushkar)\ **Replies:** 2\ **Last updated:** [January 30, 2020, 8:06pm UTC](https://forum.allencell.org/t/separating-zstacks-into-individual-cells/167 "2020-01-30T20:06:18Z")
I saw that you used .npz files in the notebook on cell shape analysis. How can I go from, say segmenting fibrous actin(same workflow as tight junction protein) to separating each individual cell ? --- ## [Distance Transform 3D](https://forum.allencell.org/t/distance-transform-3d/159)
**Author:** [@dylanmendonca](https://forum.allencell.org/u/dylanmendonca)\ **Replies:** 20\ **Last updated:** [January 14, 2020, 9:49pm UTC](https://forum.allencell.org/t/distance-transform-3d/159 "2020-01-14T21:49:57Z")
I noticed that you guys use distance\_transform\_edt from scipy. Does this apply to 3D structures? Also, what does min\_distance represent? I’m asking because I’m interested in counting the number of nuclei after segmentat… --- ## [Deep Learning Framework for Allen Cell Segmenter](https://forum.allencell.org/t/deep-learning-framework-for-allen-cell-segmenter/161)
**Author:** [@dylanmendonca](https://forum.allencell.org/u/dylanmendonca)\ **Replies:** 3\ **Last updated:** [January 13, 2020, 8:25pm UTC](https://forum.allencell.org/t/deep-learning-framework-for-allen-cell-segmenter/161 "2020-01-13T20:25:19Z")
Is your iterative deep learning framework based on this paper? I was also curious about how the deep learning framework was trained. Do you train using 3D cell image data that was annotated slice-by-slice? If so, do you… --- ## [Using Cell Segmenter on Cloud Server](https://forum.allencell.org/t/using-cell-segmenter-on-cloud-server/158)
**Author:** [@dylanmendonca](https://forum.allencell.org/u/dylanmendonca)\ **Replies:** 1\ **Last updated:** [December 28, 2019, 2:48am UTC](https://forum.allencell.org/t/using-cell-segmenter-on-cloud-server/158 "2019-12-28T02:48:12Z")
Hi, I really love the Cell Segmenter but I want to start using the iterative deep learning workflow on my images. However, I only have access to a GPU on a remote computational cluster called Compute Canada. I was wonde… --- ## [Segmentation, clear\_border](https://forum.allencell.org/t/segmentation-clear-border/141)
**Author:** [@ChrisPrinz](https://forum.allencell.org/u/ChrisPrinz)\ **Replies:** 6\ **Last updated:** [October 8, 2019, 11:14pm UTC](https://forum.allencell.org/t/segmentation-clear-border/141 "2019-10-08T23:14:26Z")
Hi, I am trying to use the Allen Cell Structure Segmenter on some slide images. The segmenter works and I am able to navigate it fairly well. I am trying to add in a scikit image function ‘clear\_border’ in order to remo…