bcfind.dinfo.unifi.it

Welcome — Brain cell finder 1.0 documentation

Documentation of main scripts. Code internals (for developers). Paper and additional materials. Enter search terms or a module, class or function name. Brain cell finder is a tool for fully automated localization of soma in 3D mouse brain images acquired by confocal light sheet microscopy. Given a 3D image as shown on the left, it first applies. Images for this research were produced by the Biophisics lab. The software was developed by the AI Lab. Of DINFO, Università di Firenze.

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Welcome — Brain cell finder 1.0 documentation | bcfind.dinfo.unifi.it Reviews

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Documentation of main scripts. Code internals (for developers). Paper and additional materials. Enter search terms or a module, class or function name. Brain cell finder is a tool for fully automated localization of soma in 3D mouse brain images acquired by confocal light sheet microscopy. Given a 3D image as shown on the left, it first applies. Images for this research were produced by the Biophisics lab. The software was developed by the AI Lab. Of DINFO, Università di Firenze.

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1 brain cell finder

2 download and install

3 user guide

4 quick search

5 welcome

6 semantic deconvolution

7 of lens

8 indices and tables

9 module index

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Welcome — Brain cell finder 1.0 documentation | bcfind.dinfo.unifi.it Reviews

https://bcfind.dinfo.unifi.it

Documentation of main scripts. Code internals (for developers). Paper and additional materials. Enter search terms or a module, class or function name. Brain cell finder is a tool for fully automated localization of soma in 3D mouse brain images acquired by confocal light sheet microscopy. Given a 3D image as shown on the left, it first applies. Images for this research were produced by the Biophisics lab. The software was developed by the AI Lab. Of DINFO, Università di Firenze.

INTERNAL PAGES

bcfind.dinfo.unifi.it

1

Paper and additional materials — Brain cell finder 1.0 documentation

http://bcfind.dinfo.unifi.it/additional.html

Documentation of main scripts. Code internals (for developers). Paper and additional materials. Enter search terms or a module, class or function name. Paper and additional materials. If you use this software or its results in a scientific context please cite the following paper:. Paolo Frasconi, Ludovico Silvestri, Paolo Soda, Roberto Cortini, Francesco Pavone and Giulio Iannello. Large-Scale Automated Identification of Mouse Brain Cells in Confocal Light Sheet Microscopy Images.

2

Installation — Brain cell finder 1.0 documentation

http://bcfind.dinfo.unifi.it/installation.html

Documentation of main scripts. Code internals (for developers). Paper and additional materials. Enter search terms or a module, class or function name. Sources are hosted on github. To obtain the code, clone the repository in some place in your system:. Git clone https:/ github.com/paolo-f/bcfind $. And set the following environment variables in your shell startup script:. Recent versions of the following Python packages are required for various operations:. And its dependencies (in particular Theano.

3

Python Module Index — Brain cell finder 1.0 documentation

http://bcfind.dinfo.unifi.it/py-modindex.html

Documentation of main scripts. Code internals (for developers). Paper and additional materials. Enter search terms or a module, class or function name.

4

Index — Brain cell finder 1.0 documentation

http://bcfind.dinfo.unifi.it/genindex.html

Documentation of main scripts. Code internals (for developers). Paper and additional materials. Enter search terms or a module, class or function name. Bcfind.semadec.deconvolver (module). Bcfind.semadec.imtensor (module). Center (class in bcfind.volume). CerebellumFlat (class in pyl2.cerebellum). CerebellumFlatAuto (class in pyl2.cerebellum). CerebellumFlatSupervised (class in pyl2.cerebellum). CerebellumFlatWithCat (class in pyl2.cerebellum). CerebellumFlatWithCatForAuto (class in pyl2.cerebellum).

5

Main scripts — Brain cell finder 1.0 documentation

http://bcfind.dinfo.unifi.it/scripts.html

Documentation of main scripts. Code internals (for developers). Paper and additional materials. Enter search terms or a module, class or function name. Usage: make substacks.py [-h] [- suffix SUFFIX] [- margin MARGIN] [- verbose] indir nx ny nz. Directory contaning the source stack (sequence of TIFF files). Of substacks along the X dimension. Of substacks along the Y dimension. Of substacks along the Z dimension. Overlap between adjacent substacks. Substack identifier, e.g. 100905. Directory where predic...

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ai.dinfo.unifi.it

Projects · AI@Unifi

http://ai.dinfo.unifi.it/projects.html

Bcfind is a tool for fully automated localization of soma in 3D mouse brain images acquired by confocal light sheet microscopy. The core technique in this method is supervised semantic deconvolution. Which uses a neural network to map a 3D image into a synthetic image where the visibility of specific entities of interest in the image (neural somata in this case) is enhanced and standardized. Website: http:/ bcfind.dinfo.unifi.it/. In SPIE European Conference on Biomedical Optics. A HPC infrastructure for...

ai.dinfo.unifi.it

Collaborations · AI@Unifi

http://ai.dinfo.unifi.it/collaborations.html

And Albert-Ludwigs-Universität Freiburg. Università di Trento. Università di Siena. And Universit&agrave Campus Biomedico. Università di Siena. MLOCRS (optical recognition of chemical structures). For all present and past collaborations see the following list of co-authors. Refine by co-author" ex:showMissing="false". Università di Firenze.

ai.dsi.unifi.it

Collaborations · AI@Unifi

http://ai.dsi.unifi.it/collaborations.html

And Albert-Ludwigs-Universität Freiburg. Università di Trento. Università di Siena. And Universit&agrave Campus Biomedico. Università di Siena. MLOCRS (optical recognition of chemical structures). For all present and past collaborations see the following list of co-authors. Refine by co-author" ex:showMissing="false". Università di Firenze.

ai.dsi.unifi.it

Projects · AI@Unifi

http://ai.dsi.unifi.it/projects.html

Bcfind is a tool for fully automated localization of soma in 3D mouse brain images acquired by confocal light sheet microscopy. The core technique in this method is supervised semantic deconvolution. Which uses a neural network to map a 3D image into a synthetic image where the visibility of specific entities of interest in the image (neural somata in this case) is enhanced and standardized. Website: http:/ bcfind.dinfo.unifi.it/. In SPIE European Conference on Biomedical Optics. A HPC infrastructure for...

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Welcome — Brain cell finder 1.0 documentation

Documentation of main scripts. Code internals (for developers). Paper and additional materials. Enter search terms or a module, class or function name. Brain cell finder is a tool for fully automated localization of soma in 3D mouse brain images acquired by confocal light sheet microscopy. Given a 3D image as shown on the left, it first applies. Images for this research were produced by the Biophisics lab. The software was developed by the AI Lab. Of DINFO, Università di Firenze.

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