ZeBraInspector

About

ZeBraInspector is a free tool for automatic analysis of 5dpf zebrafish larvae allowing:

  • realignment of the samples for a better comparison between them following screenshot captures ;
  • whole larva and white matter segmentation requesting a lipophilic dye staining ;
  • automatic creation of an excel sheet including results of the volumetric analysis.

Citation: ZeBraInspector, a whole organism screening platform enabling volumetric analysis of zebrafish brain white matter.
Lempereur S, Simion M, Machado E, Licata F, Buzer L, Chatterjee P, De Crozé N, Léonard M, Affaticati P, Jenett A, Talbot H, Joly JS.

You can access the user guide for the software by clicking on the “?” icon in the main menu.

NB: If your computer does not run the ZeBraInspector (Fatal error window when launching), please try to install Microsoft Visual C++ 2017.

A security window might appear.

License: GNU General Public License


Additionnal packages:

Two single-channel images (nd2 format) of 5D zebrafish larvae stained with a lipophilic dye using a fast protocol (refer to Fig.2 and Material and Methods in Lempereur et al.)

Ten single-channel images (mha format) of 5D zebrafish larvae used to tune whole-body and white matter segmentation (refer to Fig.6/7 and Material and Methods in Lempereur et al.)

Two dual-channel images (nd2 format) of 5D zebrafish larvae.

Channel 0: lipophilic dye staining of mutant larvae depleted of pigments on the body but with pigmented eyes. No depigmented protocol is applied to these larvae. Hence native fluorescent is preserved, but eyes remain pigmented. To register these images, the “pigmented eyes” option should be selected.

Channel 1: native RFP fluorescent staining in vessels (kdlr promoter). Refer to protocol preserving native fluorescence in Lempereur et al.

Two dual-channel images (nd2 format) of 5D zebafish larvae.

Channel 0: lipophilic dye staining.

Channel 1: anti-HuC antibody staining.  Fish are depigmented by a chemical treatment. Refer to Hu-C immunolabelling protocol in Lempereur et al.

Two three-channel images of 5D zebrafish larvae.

Channel 0: vessels stained in green.

Channel 1: lipophilic dye.

Channel 2: injected red Sindbis virus particle.

To register these images, Channel 1 should be selected as reference channel. Refer to anti-GFP and anti RFP protocol in Material and Methods in Lempereur et al.

A collection of 48 monocanal pictures (DiI staining) to estimate time for loading such big data, for registration, segmentation of whole-body and brain white-matter, and brain volumetry computation.