Useful resources for each step of the 3D imaging pipeline
| . | Resource . | Description . |
|---|---|---|
| Tissue clearing and labeling | https://idisco.info/ | From the inventors of iDISCO; updated protocols and useful tips, including a list of validated antibodies. |
| https://transparent-human-embryo.com/ | From the inventors of 3DISCO; collection of 3D datasets of human embryos and fetuses, protocols with useful tips, including a list of validated antibodies. | |
| https://clearlightbiotechnologies.com/ | Company founded by the inventor of CLARITY, providing consulting services for CLARITY tissue clearing, including a list of antibodies optimized for thick tissue penetration. | |
| http://discotechnologies.org/ | Compilation of resources for protocols of the DISCO family, including didactic demonstration videos. | |
| http://cubic.riken.jp/ | From the inventors of CUBIC; updated protocols with useful tips. | |
| Richardson and Lichtman (2015) | An essential reference on the physicochemical principle of the various tissue-clearing methods. | |
| Parra-Damas and Saura (2020) | Review article on tissue-clearing applications for the study of neuropathological processes. It includes a useful table summarizing the key features of the main tissue-clearing methods. | |
| Ueda et al. (2020b) | Review article on tissue-clearing applications in neuroscience. It includes a useful table compiling tissue-clearing reagents and their role in the process. | |
| Richardson et al. (2021) | An essential primer describing a modular approach to tissue clearing to rationally design a customized clearing protocol according to the specificities of the sample. | |
| Vieites-Prado and Renier (2021) | Extensive review article on tissue-clearing applications in developmental biology. It includes a useful table of tissue-clearing methods with their pros and cons, guidelines to choose an adequate method, a figure illustrating a modular vision of tissue clearing with the various reagents that can be used for each module, and a table summarizing model species analyzed with tissue clearing. | |
| Weiss et al. (2021) | Tutorial describing the challenges associated with tissue clearing and providing valuable recommendations to optimize sample preparation and imaging. It includes a very interesting figure illustrating classical artifacts encountered when imaging cleared samples with LSFM. | |
| Light sheet microscopy | Ariel (2018) | This guide written for users of the LaVision Biotec Ultramicroscope II system (now Miltenyi Biotec) compiles a lot of valuable considerations and recommendations, many of which apply generally to LSFM. |
| Olarte et al. (2018) | (Very) comprehensive review for readers interested in LSFM from an optics perspective. It presents guidelines for designing a customized LSFM, various system architectures, and strategies to push forward the resolution limits. It also provides a table comparing the key features of commercial LSFM systems. | |
| Ueda et al. (2020b) | (Already mentioned for tissue clearing.) It includes a very useful figure comparing the resolution, speed, and working distance of custom and commercial LSFM systems. | |
| Image analysis | Reynaud et al. (2015) | A commentary on the challenges associated with LSFM and the interdisciplinarity required by the technique. It includes valuable recommendations for image processing and for handling the huge volume of data generated. |
| Gibbs et al. (2021) | An essential review of LSFM image analysis software. It presents basic computing concepts required to develop an image analysis pipeline and provides guidelines to select an adequate analysis tool. It includes several useful figures, such as an illustration of the range of light-sheet data sizes, computing environments, and processing tasks and an overview of the hardware/software solutions employed by several research groups. |
| . | Resource . | Description . |
|---|---|---|
| Tissue clearing and labeling | https://idisco.info/ | From the inventors of iDISCO; updated protocols and useful tips, including a list of validated antibodies. |
| https://transparent-human-embryo.com/ | From the inventors of 3DISCO; collection of 3D datasets of human embryos and fetuses, protocols with useful tips, including a list of validated antibodies. | |
| https://clearlightbiotechnologies.com/ | Company founded by the inventor of CLARITY, providing consulting services for CLARITY tissue clearing, including a list of antibodies optimized for thick tissue penetration. | |
| http://discotechnologies.org/ | Compilation of resources for protocols of the DISCO family, including didactic demonstration videos. | |
| http://cubic.riken.jp/ | From the inventors of CUBIC; updated protocols with useful tips. | |
| Richardson and Lichtman (2015) | An essential reference on the physicochemical principle of the various tissue-clearing methods. | |
| Parra-Damas and Saura (2020) | Review article on tissue-clearing applications for the study of neuropathological processes. It includes a useful table summarizing the key features of the main tissue-clearing methods. | |
| Ueda et al. (2020b) | Review article on tissue-clearing applications in neuroscience. It includes a useful table compiling tissue-clearing reagents and their role in the process. | |
| Richardson et al. (2021) | An essential primer describing a modular approach to tissue clearing to rationally design a customized clearing protocol according to the specificities of the sample. | |
| Vieites-Prado and Renier (2021) | Extensive review article on tissue-clearing applications in developmental biology. It includes a useful table of tissue-clearing methods with their pros and cons, guidelines to choose an adequate method, a figure illustrating a modular vision of tissue clearing with the various reagents that can be used for each module, and a table summarizing model species analyzed with tissue clearing. | |
| Weiss et al. (2021) | Tutorial describing the challenges associated with tissue clearing and providing valuable recommendations to optimize sample preparation and imaging. It includes a very interesting figure illustrating classical artifacts encountered when imaging cleared samples with LSFM. | |
| Light sheet microscopy | Ariel (2018) | This guide written for users of the LaVision Biotec Ultramicroscope II system (now Miltenyi Biotec) compiles a lot of valuable considerations and recommendations, many of which apply generally to LSFM. |
| Olarte et al. (2018) | (Very) comprehensive review for readers interested in LSFM from an optics perspective. It presents guidelines for designing a customized LSFM, various system architectures, and strategies to push forward the resolution limits. It also provides a table comparing the key features of commercial LSFM systems. | |
| Ueda et al. (2020b) | (Already mentioned for tissue clearing.) It includes a very useful figure comparing the resolution, speed, and working distance of custom and commercial LSFM systems. | |
| Image analysis | Reynaud et al. (2015) | A commentary on the challenges associated with LSFM and the interdisciplinarity required by the technique. It includes valuable recommendations for image processing and for handling the huge volume of data generated. |
| Gibbs et al. (2021) | An essential review of LSFM image analysis software. It presents basic computing concepts required to develop an image analysis pipeline and provides guidelines to select an adequate analysis tool. It includes several useful figures, such as an illustration of the range of light-sheet data sizes, computing environments, and processing tasks and an overview of the hardware/software solutions employed by several research groups. |