SmRG algorithm - a smart region growing for 3D neuron segmentation

Accurately mapping the brain at the micro-scale is still a challenge in cellular neuroscience. While notable success has been reached in the field of tissue clarification and confocal imaging to obtain high-fidelity maps of three-dimensional neuron organization, neuron segmentation is still far away of ground-truth and sometimes manual segmentation performed by experts may be needed.

ManSegTool

ManSegTool is short for "MANual SEGmentation TOOL" software.

CNR & MPI tool

CNR & MPI tool is a user-friendly software developed for the evaluation of the image quality in both RGB and image stacks aquired using a confocal microscope.

 

CrEAP tool

CrEAP is a user-friendly tool developed for the evaluation of the displacement of optical trackers on a membrane during the stretching.

 

STEGUN* DOWNLOAD

S.T.E.GU.N. (acronyms for Slice Thickness Evaluation GUi for Non-expert users) is an open-source tool  developed in Matlab (the MathWorks-sTM Inc., Massachusetts, USA).

Developed at the Research Center  "E. Piaggio", University of Pisa, the freeware can be downloaded at this link and the source code can be download at this link.

HisTOOLogy download

Developed at the Research Center  "E. Piaggio", University of Pisa, the freeware (and few images we used to validate the tool) can  be downloaded at this link. The source code can be downloaded at this link.

Sphyga downloads

Sphyga (acronism for SPherical HYdrogel Generator) is a compact open-source tool for the fabrication of highly reproducible hydrogel based microbeads with predictable shapes and diameters ranging from 100 to 2000 µm.