Software & Code


AGAVE *Notice: Please start new topics/posts on image.sc since we have joined them as a community partner! Miscellaneous For topics that do not belong to other existing categories. 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. Segmenter *Notice: Please start new topics/posts on image.sc since we have joined them as a community partner! 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
0 856 October 3, 2018
Questions about the use of AGEA
Software & Code
0 403 April 4, 2022
Has anyone tried running the ML code on a cluster?
Software & Code
5 206 January 23, 2022
Error when read image with AICSImage
Software & Code
2 197 November 8, 2021
3D single cell image data set
Segmenter
segmentation ,  segmenter ,  napari
12 307 October 27, 2021
"setup.py" not found error
Segmenter
getting-started ,  segmenter
1 178 September 9, 2021
Iterative Deep Learning Workflow
Segmenter
10 340 August 20, 2021
Playground 9: Segmentation workflows for lamin b1 (interphase)
Segmenter
segmentation
13 419 June 9, 2021
Saving orientation and zoom for 3d Stack
AGAVE
agave
4 336 June 3, 2021
Image rotation animation
AGAVE
2 232 May 27, 2021
Segmentation error after windows update
Segmenter
segmentation
4 291 April 29, 2021
Dowload of set of naturel image to extruct features from the the ISH image of developing mouse brain
Miscellaneous
1 251 April 9, 2021
3D image analysis after classic segmentation
Segmenter
segmentation
2 333 March 23, 2021
Aicsshparam/cvapipe_analysis - questions about adding new alignment functions
Miscellaneous
1 286 March 9, 2021
Nucleus DAPI segmentation (only)
Segmenter
segmentation
8 525 February 25, 2021
Cvapipeline_analysis - Can I download a smaller dataset from Quilt to test the integrated modeling and analysis pipeline?
Download
getting-started
5 384 February 18, 2021
Image size error- Same image has different sizes on different cpus?
Segmenter
7 776 February 15, 2021
No module named 'aicssegmentation'
Segmenter
7 464 December 22, 2020
Image dimensions seem to be assigned incorrectly by aicsimageio when running deep learning segmenter
Segmenter
12 476 December 22, 2020
Simularium Bug Report for non-GitHub users
Simularium
bug-report
0 439 December 16, 2020
Network wide sourcing
Miscellaneous
0 312 November 11, 2020
Batch Processing Error
Segmenter
9 648 November 21, 2020
Opening segmentation .py files in python
Segmenter
segmentation
7 444 October 27, 2020
Errors with running the demo of the Classic Image Segmentation
Segmenter
segmentation
17 1181 September 28, 2020
Using deep learning segmenter to segment whole cells
Segmenter
segmentation
3 477 September 3, 2020
Lamin B1 Segmentation
Segmenter
segmentation
1 435 August 30, 2020
Changing the code of playground_filament3D to support a 2D image
Segmenter
1 439 August 13, 2020
The training images for the label free prediction
Miscellaneous
getting-started
1 610 August 13, 2020
Downloading LabelFree Image From Quilt
Download
cell-feature-explorer ,  getting-started
4 562 August 10, 2020
Error Loading Images in Look Up Table
Segmenter
getting-started
6 497 July 22, 2020