# Miscellaneous **URL:** https://forum.allencell.org/c/software-code/misc/19.md [Latest](https://forum.allencell.org/latest.md) · [Categories](https://forum.allencell.org/categories.md) · [Tags](https://forum.allencell.org/tags.md) --- ## [About the Miscellaneous category](https://forum.allencell.org/t/about-the-miscellaneous-category/257)
**Author:** [@cells](https://forum.allencell.org/u/cells)\ **Replies:** 0
For topics that do not belong to other existing categories. --- ## [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… --- ## [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 --- ## [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 … --- ## [Network wide sourcing](https://forum.allencell.org/t/network-wide-sourcing/266)
**Author:** [@neurona](https://forum.allencell.org/u/neurona)\ **Replies:** 0\ **Last updated:** [November 11, 2020, 7:22pm UTC](https://forum.allencell.org/t/network-wide-sourcing/266 "2020-11-11T19:22:35Z")
What are the different techniques used in Allen Brain Atlas compared to other networks that help to understand mapping? --- ## [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… --- ## [Fiji phenotyping help](https://forum.allencell.org/t/fiji-phenotyping-help/187)
**Author:** [@Patrick](https://forum.allencell.org/u/Patrick)\ **Replies:** 1\ **Last updated:** [July 22, 2020, 5:50pm UTC](https://forum.allencell.org/t/fiji-phenotyping-help/187 "2020-07-22T17:50:44Z")
Is there a tutorial or workshop or people I can ask to help me get started using Fiji to do phenotyping of tumors in mice for various fluorescent labels. My images are .im3 files from nuance. It would be helpful to be … --- ## [Viewing Voxels Using ITK Widgets](https://forum.allencell.org/t/viewing-voxels-using-itk-widgets/165)
**Author:** [@dylanmendonca](https://forum.allencell.org/u/dylanmendonca)\ **Replies:** 3\ **Last updated:** [February 12, 2020, 9:20pm UTC](https://forum.allencell.org/t/viewing-voxels-using-itk-widgets/165 "2020-02-12T21:20:08Z")
Hi, My cell images are distorted in the sense that the aspect ratios are all off. How do I incorporate the voxel size in python? When I use 3D viewer in ImageJ with the specified size, it interpolates just fine. How co… --- ## [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 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… --- ## [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…