# Software & Code **URL:** https://forum.allencell.org/c/software-code/11.md [Latest](https://forum.allencell.org/latest.md) · [Categories](https://forum.allencell.org/categories.md) · [Tags](https://forum.allencell.org/tags.md) --- ## [About the Software, Code & Imaging category](https://forum.allencell.org/t/about-the-software-code-imaging-category/52)
**Author:** [@cells](https://forum.allencell.org/u/cells)\ **Replies:** 0
This is a place to discuss label free methods, cell segmentation code, and integrated cell modeling issues and to exchange knowledge regarding the software and code we release. Topics may also include issues with images … --- ## [FNet setup issues due to outdated dependencies – any updated version or Docker?](https://forum.allencell.org/t/fnet-setup-issues-due-to-outdated-dependencies-any-updated-version-or-docker/792)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**Replies:** 5\ **Last updated:** [March 25, 2026, 11:31pm UTC](https://forum.allencell.org/t/fnet-setup-issues-due-to-outdated-dependencies-any-updated-version-or-docker/792 "2026-03-25T23:31:18Z")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… --- ## [Finding Specific Track IDs in Vol-E](https://forum.allencell.org/t/finding-specific-track-ids-in-vol-e/794)
**Author:** [@swalsh](https://forum.allencell.org/u/swalsh)\ **Replies:** 1\ **Last updated:** [March 23, 2026, 3:49am UTC](https://forum.allencell.org/t/finding-specific-track-ids-in-vol-e/794 "2026-03-23T03:49:43Z")
Hi, we have analyzed a bunch of data through TFE, and it would be nice to verify the 3D images in Vol-E. We have a list of track IDs and time stamps, and we would like to zoom in to capture images of the cells at particu… --- ## [Drug perturbation pilot study metadata is missing](https://forum.allencell.org/t/drug-perturbation-pilot-study-metadata-is-missing/788)
**Author:** [@UBio1600](https://forum.allencell.org/u/UBio1600)\ **Replies:** 3\ **Last updated:** [March 1, 2026, 1:53pm UTC](https://forum.allencell.org/t/drug-perturbation-pilot-study-metadata-is-missing/788 "2026-03-01T13:53:26Z")
Hi! I am exploring the data in Drug perturbation pilot study - ALLEN CELL EXPLORER for drug function study. However, the metadata provided in Download cell data: images, genomics, features - ALLEN CELL EXPLORER is not pe… --- ## [Cvapipe\_analysis, cannot run test case (shape analysis on 300 cells)](https://forum.allencell.org/t/cvapipe-analysis-cannot-run-test-case-shape-analysis-on-300-cells/757)
**Author:** [@lucas.philipp1](https://forum.allencell.org/u/lucas.philipp1)\ **Replies:** 1\ **Last updated:** [March 19, 2025, 11:52pm UTC](https://forum.allencell.org/t/cvapipe-analysis-cannot-run-test-case-shape-analysis-on-300-cells/757 "2025-03-19T23:52:21Z")
Description A clear description of the bug Successfully installed cvapipe\_analysis, although I had to use Python 3.9 instead of Python 3.8 as recommended. I tried running cvapipe\_analysis loaddata run --test, but the th… --- ## [Image viewer error classic segmentation jupyter notebook](https://forum.allencell.org/t/image-viewer-error-classic-segmentation-jupyter-notebook/455)
**Author:** [@AidanF](https://forum.allencell.org/u/AidanF)\ **Replies:** 4\ **Last updated:** [August 15, 2024, 10:09pm UTC](https://forum.allencell.org/t/image-viewer-error-classic-segmentation-jupyter-notebook/455 "2024-08-15T22:09:05Z")
Hi All, New error experienced when running the look up table demo via jupyter notebook (through anaconda). During the loading the data step I get the following error: Failed to parse XML for the provided file. Error: … --- ## [Is there any timelapse microscopy data for fluorescently tagged hiPSCs available for download?](https://forum.allencell.org/t/is-there-any-timelapse-microscopy-data-for-fluorescently-tagged-hipscs-available-for-download/707)
**Author:** [@cell](https://forum.allencell.org/u/cell)\ **Replies:** 1\ **Last updated:** [May 16, 2024, 7:45pm UTC](https://forum.allencell.org/t/is-there-any-timelapse-microscopy-data-for-fluorescently-tagged-hipscs-available-for-download/707 "2024-05-16T19:45:21Z")
Hi, I am new here and looking to see if there is any timelapse microscopy data available for download for the fluorescently tagged hiPSC lines. For example, is the microscopy data available for the compiled movies of som… --- ## [Why python, not imageJ?](https://forum.allencell.org/t/why-python-not-imagej/156)
**Author:** [@samuelorion](https://forum.allencell.org/u/samuelorion)\ **Replies:** 3\ **Last updated:** [March 1, 2024, 8:14am UTC](https://forum.allencell.org/t/why-python-not-imagej/156 "2024-03-01T08:14:15Z")
I am a relatively new user of automated image analysis methods. I am developing automated counting and tracing methods for multi well plates for primary neuronal cultures - using both standard and confocal microscopy. T… --- ## [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… --- ## [Segmenter training data and trained models](https://forum.allencell.org/t/segmenter-training-data-and-trained-models/675)
**Author:** [@oded](https://forum.allencell.org/u/oded)\ **Replies:** 2\ **Last updated:** [January 10, 2024, 7:42pm UTC](https://forum.allencell.org/t/segmenter-training-data-and-trained-models/675 "2024-01-10T19:42:24Z")
Hi From the tutorials on segmentation I understand that there is a pipeline to be followed. First classic segmentation is done followed by DL segmentation using the good classic results as ground truth (curation). It m… --- ## [Background on sample Data](https://forum.allencell.org/t/background-on-sample-data/672)
**Author:** [@mtu2](https://forum.allencell.org/u/mtu2)\ **Replies:** 1\ **Last updated:** [December 4, 2023, 4:51pm UTC](https://forum.allencell.org/t/background-on-sample-data/672 "2023-12-04T16:51:56Z")
Hi I want to use this example dataset I got off the page on downloading cell feature data… this is the example set…I was wondering what paper its from? --- ## [Cannot find image metadata on 'Generative Modeling with Conditional Autoencoders: Building an Integrated Cell' dataset](https://forum.allencell.org/t/cannot-find-image-metadata-on-generative-modeling-with-conditional-autoencoders-building-an-integrated-cell-dataset/662)
**Author:** [@chois](https://forum.allencell.org/u/chois)\ **Replies:** 1\ **Last updated:** [October 5, 2023, 8:41pm UTC](https://forum.allencell.org/t/cannot-find-image-metadata-on-generative-modeling-with-conditional-autoencoders-building-an-integrated-cell-dataset/662 "2023-10-05T20:41:24Z")
Hi, thank you for making available all of the beautiful datasets! I am trying to pre-process the dataset found in ‘Generative Modeling with Conditional Autoencoders: Building an Integrated Cell’ pre-print. I believe it… --- ## [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… --- ## [Watershed import error napari allen segementer](https://forum.allencell.org/t/watershed-import-error-napari-allen-segementer/452)
**Author:** [@AidanF](https://forum.allencell.org/u/AidanF)\ **Replies:** 0\ **Last updated:** [June 18, 2022, 1:51am UTC](https://forum.allencell.org/t/watershed-import-error-napari-allen-segementer/452 "2022-06-18T01:51:47Z")
Hello, I’m using the Allen Cell Segmenter via Napari and am getting the following error when using certain protocols (which include watershed): ImportError: cannot import name ‘watershed’ from ‘skimage.morphology’ (C:\\… --- ## [Image Reading Error Classic Segmenter](https://forum.allencell.org/t/image-reading-error-classic-segmenter/454)
**Author:** [@AidanF](https://forum.allencell.org/u/AidanF)\ **Replies:** 0\ **Last updated:** [June 21, 2022, 7:44pm UTC](https://forum.allencell.org/t/image-reading-error-classic-segmenter/454 "2022-06-21T19:44:35Z")
Hi all, Getting the following error when trying to segment data in jupyter notebooks: FILE\_NAME = ‘Test2.tif’ reader = AICSImage(FILE\_NAME) IMG = reader.data.astype(np.float32) print(IMG.shape) Failed to parse XML … --- ## [Error in the source code of suggest\_normalization\_param](https://forum.allencell.org/t/error-in-the-source-code-of-suggest-normalization-param/453)
**Author:** [@ashapeng](https://forum.allencell.org/u/ashapeng)\ **Replies:** 0\ **Last updated:** [June 21, 2022, 1:29am UTC](https://forum.allencell.org/t/error-in-the-source-code-of-suggest-normalization-param/453 "2022-06-21T01:29:42Z")
Hi, Our lab ran the segmentation today. there is error in the suggest\_normalization\_param. It missed a “return” line to return the low\_ratio, up\_ratio. with no return function, it couldn’t be unpacked. Thanks, Peng --- ## [Questions on AllenCellModeling/pytorch\_fnet data set](https://forum.allencell.org/t/questions-on-allencellmodeling-pytorch-fnet-data-set/447)
**Author:** [@Thomas](https://forum.allencell.org/u/Thomas)\ **Replies:** 2\ **Last updated:** [May 30, 2022, 8:18am UTC](https://forum.allencell.org/t/questions-on-allencellmodeling-pytorch-fnet-data-set/447 "2022-05-30T08:18:10Z")
I work on the data set from the Allen Insitute, used in this work, and which can be found here. In each picture you get 7 channels, with (for example) the following names: CMDRP, CMDRP, EGFP, EGFP, H3342, H3342, Bright… --- ## [Questions about the use of AGEA](https://forum.allencell.org/t/questions-about-the-use-of-agea/443)
**Author:** [@YZallen](https://forum.allencell.org/u/YZallen)\ **Replies:** 0\ **Last updated:** [April 4, 2022, 11:56am UTC](https://forum.allencell.org/t/questions-about-the-use-of-agea/443 "2022-04-04T11:56:59Z")
I have some difficulty in following the user guide manual of the AGEA, because many links and the reference article were either no longer existing (e.g. Appendix B) or did not contain the information to understand the fi… --- ## [Has anyone tried running the ML code on a cluster?](https://forum.allencell.org/t/has-anyone-tried-running-the-ml-code-on-a-cluster/360)
**Author:** [@mramsahoye](https://forum.allencell.org/u/mramsahoye)\ **Replies:** 5\ **Last updated:** [January 23, 2022, 8:55pm UTC](https://forum.allencell.org/t/has-anyone-tried-running-the-ml-code-on-a-cluster/360 "2022-01-23T20:55:23Z")
Hello there, I’m trying to get this software to run on my university’s cluster (https://hpcf.umbc.edu/) and I was wondering if anyone has tried the same and if so; how did you go about getting things to work like Jupyte… --- ## [Error when read image with AICSImage](https://forum.allencell.org/t/error-when-read-image-with-aicsimage/366)
**Author:** [@ashapeng](https://forum.allencell.org/u/ashapeng)\ **Replies:** 2\ **Last updated:** [November 8, 2021, 9:26pm UTC](https://forum.allencell.org/t/error-when-read-image-with-aicsimage/366 "2021-11-08T21:26:00Z")
Hi everyone, I got the following error when I tried to read my image. but I am able to get shape, and ndim information of my image TiffPage 0: TypeError: read\_bytes() missing 3 required positional arguments: ‘dtype’, … --- ## [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 … --- ## [Saving orientation and zoom for 3d Stack](https://forum.allencell.org/t/saving-orientation-and-zoom-for-3d-stack/324)
**Author:** [@pushkar](https://forum.allencell.org/u/pushkar)\ **Replies:** 4\ **Last updated:** [June 3, 2021, 5:33pm UTC](https://forum.allencell.org/t/saving-orientation-and-zoom-for-3d-stack/324 "2021-06-03T17:33:29Z")
Hi, AGAVE is a really good tool for visualization of 3D stacks. I want to save/ use the same values for multiple stacks for their orientation, zoom/view and scale so that they are more easy to compare. Is there a way I … --- ## [Image rotation animation](https://forum.allencell.org/t/image-rotation-animation/328)
**Author:** [@pushkar](https://forum.allencell.org/u/pushkar)\ **Replies:** 2\ **Last updated:** [May 27, 2021, 4:53pm UTC](https://forum.allencell.org/t/image-rotation-animation/328 "2021-05-27T16:53:53Z")
Hi, I was wondering if there was a way to save multiple images as a slideshow or gifs or animations. Currently I am thinking of manually rotating them slightly and saving separate images which can later be put together… --- ## [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… --- ## [Dowload of set of naturel image to extruct features from the the ISH image of developing mouse brain](https://forum.allencell.org/t/dowload-of-set-of-naturel-image-to-extruct-features-from-the-the-ish-image-of-developing-mouse-brain/310)
**Author:** [@Hanane](https://forum.allencell.org/u/Hanane)\ **Replies:** 1\ **Last updated:** [April 9, 2021, 3:46pm UTC](https://forum.allencell.org/t/dowload-of-set-of-naturel-image-to-extruct-features-from-the-the-ish-image-of-developing-mouse-brain/310 "2021-04-09T15:46:12Z")
Hi I was wondering if there is a way to dowload of set of naturel image to extruct features from the the ISH image of developing mouse brain by Deep convolutional neural network Thanks --- ## [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… --- ## [Aicsshparam/cvapipe\_analysis - questions about adding new alignment functions](https://forum.allencell.org/t/aicsshparam-cvapipe-analysis-questions-about-adding-new-alignment-functions/297)
**Author:** [@lynn](https://forum.allencell.org/u/lynn)\ **Replies:** 1\ **Last updated:** [March 9, 2021, 6:50pm UTC](https://forum.allencell.org/t/aicsshparam-cvapipe-analysis-questions-about-adding-new-alignment-functions/297 "2021-03-09T18:50:26Z")
In the cell variance paper, it is noted that the spherical harmonics coefficients are sensitive to the orientations of the cells, and that different methods of alignment can generate different versions of shape space. I … [Next page](https://forum.allencell.org/c/software-code/11.md?page=1)