Software & Code

AGAVE Advanced GPU Accelerated Volume Explorer (AGAVE) is a volume viewer that uses path-trace rendering in an interface designed and optimized for the display of multi-channel OME TIFF files. Miscellaneous For topics that do not belong to other existing categories. Segmenter The Allen Cell & Structure Segmenter is a Python-based open source toolkit developed at the Allen Institute for Cell Science for 3D segmentation of intracellular structures in fluorescence microscope images. 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. 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	666	October 3, 2018
Playground 9: Segmentation workflows for lamin b1 (interphase) Software & Code	13	171	June 9, 2021
Saving orientation and zoom for 3d Stack AGAVE agave	4	110	June 3, 2021
Image rotation animation AGAVE	2	64	May 27, 2021
Segmentation error after windows update Software & Code segmentation	4	95	April 29, 2021
Dowload of set of naturel image to extruct features from the the ISH image of developing mouse brain Software & Code	1	103	April 9, 2021
3D image analysis after classic segmentation Software & Code segmentation	2	159	March 23, 2021
Aicsshparam/cvapipe_analysis - questions about adding new alignment functions Software & Code	1	143	March 9, 2021
Nucleus DAPI segmentation (only) Software & Code	8	251	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	213	February 18, 2021
Image size error- Same image has different sizes on different cpus? Segmenter	7	569	February 15, 2021
No module named 'aicssegmentation' Software & Code	7	229	December 22, 2020
Image dimensions seem to be assigned incorrectly by aicsimageio when running deep learning segmenter Segmenter	12	306	December 22, 2020
Simularium Bug Report for non-GitHub users Simularium bug-report	0	292	December 16, 2020
Network wide sourcing Miscellaneous	0	181	November 11, 2020
Batch Processing Error Segmenter	9	449	November 21, 2020
Opening segmentation .py files in python Miscellaneous segmentation	7	264	October 27, 2020
Errors with running the demo of the Classic Image Segmentation Miscellaneous segmentation	17	855	September 28, 2020
Using deep learning segmenter to segment whole cells Segmenter segmentation	3	287	September 3, 2020
Lamin B1 Segmentation Miscellaneous segmentation	1	255	August 30, 2020
Changing the code of playground_filament3D to support a 2D image Segmenter	1	267	August 13, 2020
The training images for the label free prediction Miscellaneous getting-started	1	264	August 13, 2020
Downloading LabelFree Image From Quilt Download cell-feature-explorer , getting-started	4	343	August 10, 2020
Error Loading Images in Look Up Table Segmenter getting-started	6	312	July 22, 2020
Fiji phenotyping help Miscellaneous	1	344	July 22, 2020
Error when running Look Up Table Demo Classic Image Segmentation Segmenter	6	331	July 21, 2020
Help Downloading Package Download	3	332	June 4, 2020
Filling empty pixels in 3D segmentation Segmenter segmentation	1	390	May 13, 2020
Batch processing for segmenter tool Segmenter	8	558	May 13, 2020
Writing to a TIFF File with Voxel Spacing [Error in Codebase] Miscellaneous aiscimageio	6	422	March 6, 2020

Allen Cell Discussion Forum

Allen Cell Discussion Forum

Software & Code