A multiwell plate approach to increase the sample throughput during tissue clearing. Akiyama, F., Matsumoto, K., Yamashita, K., Oishi, A., Kitaoka, T., & Ueda, H. R Nat. Protoc., 20(4):967–988, April, 2025. ![A multiwell plate approach to increase the sample throughput during tissue clearing [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper abstract bibtex Tissue clearing, coupled with immunostaining, enables the transition from two-dimensional to three-dimensional pathology and has the potential to substantially improve data quality for biomedical diagnostics. Nevertheless, the workflows are limited by the complex sample processing protocols. Approaches for the parallel processing of samples, to include tissue clearing, immunostaining, imaging and analysis can increase three-dimensional pathology throughput. Here we detail a step-by-step approach that combines a tissue clearing device with a six-well multiwell plate to increase the throughput compared with methods using conventional clearing protocols. The six-well multiplate allows for parallel tissue clearing of multiple samples and is compatible with passive tissue clearing methods including Clear, Unobstructed Brain/Body Imaging Cocktails and Computational (CUBIC) analysis. In addition, gel embedding is performed without moving the samples from the wells, and a series of steps such as imaging with a high-speed light-sheet microscope and analysis in the cloud can be performed. Although this procedure slightly extends the overall time required for preparing and analyzing a single sample, it reduces the effort required at each step, such as reagent exchange and gel embedding, which results in an overall reduction in hands-on time due to the parallel sample processing. We describe a series of whole-organ analyses, including high-throughput tissue clearing, staining, gel embedding, imaging and data analysis in the cloud, as a useful platform for cellular biology and pathology. The total process varies depending on the presence or absence of immunostaining, but for some six-well plates, the tissue clearing process, imaging and data analysis can be completed within 10 d.
@ARTICLE{Akiyama2025-ua,
title = "A multiwell plate approach to increase the sample throughput
during tissue clearing",
author = "Akiyama, Fumito and Matsumoto, Katsuhiko and Yamashita, Katsunari
and Oishi, Akio and Kitaoka, Takashi and Ueda, Hiroki R",
journal = "Nat. Protoc.",
volume = 20,
number = 4,
pages = "967--988",
abstract = "Tissue clearing, coupled with immunostaining, enables the
transition from two-dimensional to three-dimensional pathology and
has the potential to substantially improve data quality for
biomedical diagnostics. Nevertheless, the workflows are limited by
the complex sample processing protocols. Approaches for the
parallel processing of samples, to include tissue clearing,
immunostaining, imaging and analysis can increase
three-dimensional pathology throughput. Here we detail a
step-by-step approach that combines a tissue clearing device with
a six-well multiwell plate to increase the throughput compared
with methods using conventional clearing protocols. The six-well
multiplate allows for parallel tissue clearing of multiple samples
and is compatible with passive tissue clearing methods including
Clear, Unobstructed Brain/Body Imaging Cocktails and Computational
(CUBIC) analysis. In addition, gel embedding is performed without
moving the samples from the wells, and a series of steps such as
imaging with a high-speed light-sheet microscope and analysis in
the cloud can be performed. Although this procedure slightly
extends the overall time required for preparing and analyzing a
single sample, it reduces the effort required at each step, such
as reagent exchange and gel embedding, which results in an overall
reduction in hands-on time due to the parallel sample processing.
We describe a series of whole-organ analyses, including
high-throughput tissue clearing, staining, gel embedding, imaging
and data analysis in the cloud, as a useful platform for cellular
biology and pathology. The total process varies depending on the
presence or absence of immunostaining, but for some six-well
plates, the tissue clearing process, imaging and data analysis can
be completed within 10 d.",
month = apr,
year = 2025,
url = "http://dx.doi.org/10.1038/s41596-024-01080-1",
file = "All Papers/A/Akiyama et al. 2025 - A multiwell plate approach to increase the sample throughput during tissue clearing.pdf",
keywords = "Laboratory publication;Laboratory publication/Since2021",
language = "en"
}
Downloads: 0
{"_id":"p642EojNzg3KjKiwL","bibbaseid":"akiyama-matsumoto-yamashita-oishi-kitaoka-ueda-amultiwellplateapproachtoincreasethesamplethroughputduringtissueclearing-2025","author_short":["Akiyama, F.","Matsumoto, K.","Yamashita, K.","Oishi, A.","Kitaoka, T.","Ueda, H. R"],"bibdata":{"bibtype":"article","type":"article","title":"A multiwell plate approach to increase the sample throughput during tissue clearing","author":[{"propositions":[],"lastnames":["Akiyama"],"firstnames":["Fumito"],"suffixes":[]},{"propositions":[],"lastnames":["Matsumoto"],"firstnames":["Katsuhiko"],"suffixes":[]},{"propositions":[],"lastnames":["Yamashita"],"firstnames":["Katsunari"],"suffixes":[]},{"propositions":[],"lastnames":["Oishi"],"firstnames":["Akio"],"suffixes":[]},{"propositions":[],"lastnames":["Kitaoka"],"firstnames":["Takashi"],"suffixes":[]},{"propositions":[],"lastnames":["Ueda"],"firstnames":["Hiroki","R"],"suffixes":[]}],"journal":"Nat. Protoc.","volume":"20","number":"4","pages":"967–988","abstract":"Tissue clearing, coupled with immunostaining, enables the transition from two-dimensional to three-dimensional pathology and has the potential to substantially improve data quality for biomedical diagnostics. Nevertheless, the workflows are limited by the complex sample processing protocols. Approaches for the parallel processing of samples, to include tissue clearing, immunostaining, imaging and analysis can increase three-dimensional pathology throughput. Here we detail a step-by-step approach that combines a tissue clearing device with a six-well multiwell plate to increase the throughput compared with methods using conventional clearing protocols. The six-well multiplate allows for parallel tissue clearing of multiple samples and is compatible with passive tissue clearing methods including Clear, Unobstructed Brain/Body Imaging Cocktails and Computational (CUBIC) analysis. In addition, gel embedding is performed without moving the samples from the wells, and a series of steps such as imaging with a high-speed light-sheet microscope and analysis in the cloud can be performed. Although this procedure slightly extends the overall time required for preparing and analyzing a single sample, it reduces the effort required at each step, such as reagent exchange and gel embedding, which results in an overall reduction in hands-on time due to the parallel sample processing. We describe a series of whole-organ analyses, including high-throughput tissue clearing, staining, gel embedding, imaging and data analysis in the cloud, as a useful platform for cellular biology and pathology. The total process varies depending on the presence or absence of immunostaining, but for some six-well plates, the tissue clearing process, imaging and data analysis can be completed within 10 d.","month":"April","year":"2025","url":"http://dx.doi.org/10.1038/s41596-024-01080-1","file":"All Papers/A/Akiyama et al. 2025 - A multiwell plate approach to increase the sample throughput during tissue clearing.pdf","keywords":"Laboratory publication;Laboratory publication/Since2021","language":"en","bibtex":"@ARTICLE{Akiyama2025-ua,\r\n title = \"A multiwell plate approach to increase the sample throughput\r\n during tissue clearing\",\r\n author = \"Akiyama, Fumito and Matsumoto, Katsuhiko and Yamashita, Katsunari\r\n and Oishi, Akio and Kitaoka, Takashi and Ueda, Hiroki R\",\r\n journal = \"Nat. Protoc.\",\r\n volume = 20,\r\n number = 4,\r\n pages = \"967--988\",\r\n abstract = \"Tissue clearing, coupled with immunostaining, enables the\r\n transition from two-dimensional to three-dimensional pathology and\r\n has the potential to substantially improve data quality for\r\n biomedical diagnostics. Nevertheless, the workflows are limited by\r\n the complex sample processing protocols. Approaches for the\r\n parallel processing of samples, to include tissue clearing,\r\n immunostaining, imaging and analysis can increase\r\n three-dimensional pathology throughput. Here we detail a\r\n step-by-step approach that combines a tissue clearing device with\r\n a six-well multiwell plate to increase the throughput compared\r\n with methods using conventional clearing protocols. The six-well\r\n multiplate allows for parallel tissue clearing of multiple samples\r\n and is compatible with passive tissue clearing methods including\r\n Clear, Unobstructed Brain/Body Imaging Cocktails and Computational\r\n (CUBIC) analysis. In addition, gel embedding is performed without\r\n moving the samples from the wells, and a series of steps such as\r\n imaging with a high-speed light-sheet microscope and analysis in\r\n the cloud can be performed. Although this procedure slightly\r\n extends the overall time required for preparing and analyzing a\r\n single sample, it reduces the effort required at each step, such\r\n as reagent exchange and gel embedding, which results in an overall\r\n reduction in hands-on time due to the parallel sample processing.\r\n We describe a series of whole-organ analyses, including\r\n high-throughput tissue clearing, staining, gel embedding, imaging\r\n and data analysis in the cloud, as a useful platform for cellular\r\n biology and pathology. The total process varies depending on the\r\n presence or absence of immunostaining, but for some six-well\r\n plates, the tissue clearing process, imaging and data analysis can\r\n be completed within 10 d.\",\r\n month = apr,\r\n year = 2025,\r\n url = \"http://dx.doi.org/10.1038/s41596-024-01080-1\",\r\n file = \"All Papers/A/Akiyama et al. 2025 - A multiwell plate approach to increase the sample throughput during tissue clearing.pdf\",\r\n keywords = \"Laboratory publication;Laboratory publication/Since2021\",\r\n language = \"en\"\r\n}\r\n\r\n","author_short":["Akiyama, F.","Matsumoto, K.","Yamashita, K.","Oishi, A.","Kitaoka, T.","Ueda, H. R"],"key":"Akiyama2025-ua","id":"Akiyama2025-ua","bibbaseid":"akiyama-matsumoto-yamashita-oishi-kitaoka-ueda-amultiwellplateapproachtoincreasethesamplethroughputduringtissueclearing-2025","role":"author","urls":{"Paper":"http://dx.doi.org/10.1038/s41596-024-01080-1"},"keyword":["Laboratory publication;Laboratory publication/Since2021"],"metadata":{"authorlinks":{}}},"bibtype":"article","biburl":"https://www.med.kurume-u.ac.jp/med/systems-biology/publications.bib","dataSources":["qtdRCccwwh4hcbEWL"],"keywords":["laboratory publication;laboratory publication/since2021"],"search_terms":["multiwell","plate","approach","increase","sample","throughput","during","tissue","clearing","akiyama","matsumoto","yamashita","oishi","kitaoka","ueda"],"title":"A multiwell plate approach to increase the sample throughput during tissue clearing","year":2025}