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. 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. Segmenter *Notice: Please start new topics/posts on image.sc since we have joined them as a community partner! 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.

Topic	Replies	Views	Activity
About the Software, Code & Imaging category Software & Code about , simularium , segmentation , agave , cell-feature-explorer	0	742	October 3, 2018
3D single cell image data set Segmenter segmentation , segmenter , napari	12	108	October 27, 2021
Has anyone tried running the ML code on a cluster? Software & Code	1	17	October 22, 2021
"setup.py" not found error Segmenter getting-started , segmenter	1	70	September 9, 2021
Iterative Deep Learning Workflow Segmenter	10	164	August 20, 2021
Playground 9: Segmentation workflows for lamin b1 (interphase) Segmenter segmentation	13	257	June 9, 2021
Saving orientation and zoom for 3d Stack AGAVE agave	4	182	June 3, 2021
Image rotation animation AGAVE	2	131	May 27, 2021
Segmentation error after windows update Segmenter segmentation	4	162	April 29, 2021
Dowload of set of naturel image to extruct features from the the ISH image of developing mouse brain Miscellaneous	1	164	April 9, 2021
3D image analysis after classic segmentation Segmenter segmentation	2	224	March 23, 2021
Aicsshparam/cvapipe_analysis - questions about adding new alignment functions Miscellaneous	1	197	March 9, 2021
Nucleus DAPI segmentation (only) Segmenter segmentation	8	326	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	278	February 18, 2021
Image size error- Same image has different sizes on different cpus? Segmenter	7	644	February 15, 2021
No module named 'aicssegmentation' Segmenter	7	329	December 22, 2020
Image dimensions seem to be assigned incorrectly by aicsimageio when running deep learning segmenter Segmenter	12	375	December 22, 2020
Simularium Bug Report for non-GitHub users Simularium bug-report	0	339	December 16, 2020
Network wide sourcing Miscellaneous	0	230	November 11, 2020
Batch Processing Error Segmenter	9	524	November 21, 2020
Opening segmentation .py files in python Segmenter segmentation	7	328	October 27, 2020
Errors with running the demo of the Classic Image Segmentation Segmenter segmentation	17	962	September 28, 2020
Using deep learning segmenter to segment whole cells Segmenter segmentation	3	353	September 3, 2020
Lamin B1 Segmentation Segmenter segmentation	1	318	August 30, 2020
Changing the code of playground_filament3D to support a 2D image Segmenter	1	329	August 13, 2020
The training images for the label free prediction Miscellaneous getting-started	1	379	August 13, 2020
Downloading LabelFree Image From Quilt Download cell-feature-explorer , getting-started	4	415	August 10, 2020
Error Loading Images in Look Up Table Segmenter getting-started	6	383	July 22, 2020
Fiji phenotyping help Miscellaneous	1	397	July 22, 2020
Error when running Look Up Table Demo Classic Image Segmentation Segmenter	6	396	July 21, 2020

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Allen Cell Discussion Forum

Software & Code