# Software & Code **URL:** https://forum.allencell.org/c/software-code/11.md?page=2 [Latest](https://forum.allencell.org/latest.md) · [Categories](https://forum.allencell.org/categories.md) · [Tags](https://forum.allencell.org/tags.md) **Page:** 3 --- ## [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… --- ## [3D Visualization Workshop - Oct 1st 2019](https://forum.allencell.org/t/3d-visualization-workshop-oct-1st-2019/117)
**Author:** [@ThaoDo](https://forum.allencell.org/u/ThaoDo)\ **Replies:** 7\ **Last updated:** [December 28, 2019, 2:51am UTC](https://forum.allencell.org/t/3d-visualization-workshop-oct-1st-2019/117 "2019-12-28T02:51:37Z")
For attendees of the 3D Visualization Workshop, which is a part of the BioImage Informatics 2019 conference held at the Allen Institute for Cell Science, if you have any questions during the workshop, we have helpers wit… --- ## [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… --- ## [Using cellprofiler in place of diameterJ?](https://forum.allencell.org/t/using-cellprofiler-in-place-of-diameterj/148)
**Author:** [@amycaitriona](https://forum.allencell.org/u/amycaitriona)\ **Replies:** 2\ **Last updated:** [November 13, 2019, 12:48am UTC](https://forum.allencell.org/t/using-cellprofiler-in-place-of-diameterj/148 "2019-11-13T00:48:22Z")
Does anyone know if using something like the analyse skeleton option on the cellprofiler pipeline can provide the same results as diameterJ on imageJ? I am quantifying vascular networks in 3D and to get density, branchin… --- ## [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… --- ## [Axes in Cell Feature Explorer](https://forum.allencell.org/t/axes-in-cell-feature-explorer/118)
**Author:** [@cells](https://forum.allencell.org/u/cells)\ **Replies:** 2\ **Last updated:** [October 1, 2019, 10:23pm UTC](https://forum.allencell.org/t/axes-in-cell-feature-explorer/118 "2019-10-01T22:23:15Z")
I would like to ask about the features in the Cell Feature Explorer. One of the available axes to choose from for the graph is cell segmentation (-1, 0, 1). What does each of the number represents in the terms of cell se… --- ## [3D cell segmentation pipeline](https://forum.allencell.org/t/3d-cell-segmentation-pipeline/96)
**Author:** [@Joel\_Luethi](https://forum.allencell.org/u/Joel_Luethi)\ **Replies:** 1\ **Last updated:** [August 6, 2019, 11:00pm UTC](https://forum.allencell.org/t/3d-cell-segmentation-pipeline/96 "2019-08-06T23:00:14Z")
You have published this really cool Segmenter for subcellular structure segmentations. I also saw that you have been using images of single cells, e.g. in the integrated cell models and in the Cell Viewer. I assume those… [Previous page](https://forum.allencell.org/c/software-code/11.md?page=1)