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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
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TissueCyte Image QC Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bbybipsn | BICCN, Allen Institute for Brain Science | This protocol describes the QC step that occurs after the week of TissueCyte runs, and prior to analysis. | Allen Institute | 1 | 2020 | Allen Institute for Brain Science 2020. TissueCyte Image QC. protocols.io dx.doi.org/10.17504/protocols.io.bbybipsn | 2021-03-29 03:14:37 | |||
|
Artificial Cerebrospinal Fluid I (ACSF.I) Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bezkjf4w | BICCN, Allen Institute for Brain Science | This protocol is used to prepare Artificial Cerebrospinal Fluid I (ACSF.I). ACSF.I is used for applications including transcardial perfusion prior to fresh mouse brain slicing and as a bathing solution during fresh mouse brain slicing. Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. | Allen Institute | 1 | 2020 | Allen Institute for Brain Science 2020. Artificial Cerebrospinal Fluid I (ACSF.I). protocols.io dx.doi.org/10.17504/protocols.io.bezkjf4w | 2021-03-29 03:14:41 | |||
|
3D Reconstruction of Neurons in Vaa3D Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bdppi5mn | BICCN, Allen Institute for Brain Science | This protocol is used to generate accurate digital representations of neuron morphologies from a variety of brain regions and species. Each reconstruction captures the positions and thicknesses of the soma, dendrites and axon of a biocytin-filled cell within a slice of brain tissue. To generate the reconstruction we use an image stack containing ~200-700 serial 2D images that captures the full extent of the cell within the slice. We use the Vaa3D (Terafly) program with a Kazom’s Mozak user interface (Mozak for short) to visualize the 2D images in 3D. Once the stack is loaded in Mozak, our reconstruction is generated by placing nodes in 3D space. The placement of these nodes is dependent on the signal in the images. Our final output, an SWC text file (.swc format), contains many thousand rows. Each row contains a node ID, an x, y, z coordinate, radius value, neurite type, and parent node ID. After tracing is complete, we preform post processing to provide radius values, check for errors and consistency then the SWCs are uploaded into our Laboratory Information Management System.Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. | Allen Institute | 2 | 2020 | Allen Institute for Brain Science 2020. 3D Reconstruction of Neurons in Vaa3D. protocols.io dx.doi.org/10.17504/protocols.io.bdppi5mn | 2021-03-29 03:14:52 | |||
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Artificial Cerebrospinal Fluid III (ACSF.III) Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.beptjdnn | BICCN, Allen Institute for Brain Science | Artificial Cerebrospinal Fluid III (ACSF.III) is used for applications including tissue bath solution during electrophysiological recording.Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. | Allen Institute | 3 | 2020 | Allen Institute for Brain Science 2020. Artificial Cerebrospinal Fluid III (ACSF.III). protocols.io dx.doi.org/10.17504/protocols.io.beptjdnn | 2021-03-29 03:14:49 | |||
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Stereotaxic Surgery for Delivery of Tracers by Iontophoresis Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bgpvjvn6 | BICCN, Allen Institute for Brain Science | This protocol describes the delivery of a neuronal tracer using the iontophoretic method. The surgery uses a stereotaxic system to target specific brain coordinates in the mouse. Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. | Allen Institute | 3 | 2020 | Allen Institute for Brain Science 2020. Stereotaxic Surgery for Delivery of Tracers by Iontophoresis. protocols.io dx.doi.org/10.17504/protocols.io.bgpvjvn6 | 2021-03-29 03:14:56 | |||
|
Maintenance of TissueCyte System Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bdpui5nw | BICCN, Allen Institute for Brain Science | This protocols provides detailed instructions for procedures needed for maintenance of the TissueCyte scanning systems.Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. | Allen Institute | 2 | 2020 | Allen Institute for Brain Science 2020. Maintenance of TissueCyte System. protocols.io dx.doi.org/10.17504/protocols.io.bdpui5nw | 2021-03-29 03:15:04 | |||
|
TissueCyte Image QC Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bdpri5m6 | BICCN, Allen Institute for Brain Science | This protocol describes the QC step that occurs after the week of TissueCyte runs, and prior to analysis.Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. | Allen Institute | 2 | 2020 | Allen Institute for Brain Science 2020. TissueCyte Image QC. protocols.io dx.doi.org/10.17504/protocols.io.bdpri5m6 | 2021-03-29 03:12:08 | |||
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BD FACS Aria II Start-up and Calibration Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.besajeae | BICCN, Allen Institute for Brain Science | This protocol provides step by step instructions for performing single-cell sorting by using BD FACSAria II machine and BD FACSDiva software in preparation for single-cell sorting.Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. | Allen Institute | 3 | 2020 | Allen Institute for Brain Science 2020. BD FACS Aria II Start-up and Calibration. protocols.io dx.doi.org/10.17504/protocols.io.besajeae | 2021-03-29 03:12:09 | |||
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Multi-Patch Clamp Recording Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bdpgi5jw | BICCN, Allen Institute for Brain Science | This protocol describes the process to obtain multiple electrophysiological recordings from postnatal mouse and/or human brain slices.Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. | Allen Institute | 2 | 2020 | Allen Institute for Brain Science 2020. Multi-Patch Clamp Recording. protocols.io dx.doi.org/10.17504/protocols.io.bdpgi5jw | 2021-03-29 03:12:08 |
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