Software & Code


Miscellaneous For topics that do not belong to other existing categories. AGAVE *Notice: Please start new topics/posts on image.sc since we have joined them as a community partner! Segmenter *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. Simularium The project Simularium aims to involve the wider biology community in building and analyzing spatial mechanistic simulations at different levels of scale and connecting them in the context of whole cells. This is a place to discuss Simularium issues and to exchange knowledge regarding the software & code we release. Download For topics related to data, software, and document downloads that the Allen Institute of Cell Science provides via our website allencell.org and other access points.
Topic Replies Views Activity
About the Software, Code & Imaging category
Software & Code
about ,  simularium ,  segmentation ,  agave ,  cell-feature-explorer
0 912 October 3, 2018
Watershed import error napari allen segementer
Software & Code
napari-allencell-segmenter ,  napari ,  segmentation ,  segmenter
0 54 June 18, 2022
Image Reading Error Classic Segmenter
Software & Code
segmenter ,  segmentation
0 52 June 21, 2022
Image viewer error classic segmentation jupyter notebook
Software & Code
segmenter
0 55 June 28, 2022
Error in the source code of suggest_normalization_param
Software & Code
segmentation
0 47 June 21, 2022
Questions on AllenCellModeling/pytorch_fnet data set
Software & Code
2 72 May 30, 2022
Questions about the use of AGEA
Software & Code
0 453 April 4, 2022
Has anyone tried running the ML code on a cluster?
Software & Code
5 276 January 23, 2022
Error when read image with AICSImage
Software & Code
2 338 November 8, 2021
3D single cell image data set
Segmenter
segmentation ,  segmenter ,  napari
12 392 October 27, 2021
"setup.py" not found error
Segmenter
getting-started ,  segmenter
1 237 September 9, 2021
Iterative Deep Learning Workflow
Segmenter
10 425 August 20, 2021
Playground 9: Segmentation workflows for lamin b1 (interphase)
Segmenter
segmentation
13 506 June 9, 2021
Saving orientation and zoom for 3d Stack
AGAVE
agave
4 475 June 3, 2021
Image rotation animation
AGAVE
2 286 May 27, 2021
Segmentation error after windows update
Segmenter
segmentation
4 347 April 29, 2021
Dowload of set of naturel image to extruct features from the the ISH image of developing mouse brain
Miscellaneous
1 296 April 9, 2021
3D image analysis after classic segmentation
Segmenter
segmentation
2 408 March 23, 2021
Aicsshparam/cvapipe_analysis - questions about adding new alignment functions
Miscellaneous
1 335 March 9, 2021
Nucleus DAPI segmentation (only)
Segmenter
segmentation
8 586 February 25, 2021
Cvapipeline_analysis - Can I download a smaller dataset from Quilt to test the integrated modeling and analysis pipeline?
Download
getting-started
5 431 February 18, 2021
Image size error- Same image has different sizes on different cpus?
Segmenter
7 844 February 15, 2021
No module named 'aicssegmentation'
Segmenter
7 542 December 22, 2020
Image dimensions seem to be assigned incorrectly by aicsimageio when running deep learning segmenter
Segmenter
12 555 December 22, 2020
Simularium Bug Report for non-GitHub users
Simularium
bug-report
0 489 December 16, 2020
Network wide sourcing
Miscellaneous
0 359 November 11, 2020
Batch Processing Error
Segmenter
9 705 November 21, 2020
Opening segmentation .py files in python
Segmenter
segmentation
7 507 October 27, 2020
Errors with running the demo of the Classic Image Segmentation
Segmenter
segmentation
17 1327 September 28, 2020
Using deep learning segmenter to segment whole cells
Segmenter
segmentation
3 551 September 3, 2020