# Science **URL:** https://community.brain-map.org/c/science/9.md?page=2 [Latest](https://community.brain-map.org/latest.md) · [Categories](https://community.brain-map.org/categories.md) · [Tags](https://community.brain-map.org/tags.md) **Page:** 3 --- ## [Voltage clamp recordings for Na channels in DRG](https://community.brain-map.org/t/voltage-clamp-recordings-for-na-channels-in-drg/2466)
**Author:** [@007](https://community.brain-map.org/u/007)\ **Replies:** 0\ **Last updated:** [July 12, 2023, 5:18pm UTC](https://community.brain-map.org/t/voltage-clamp-recordings-for-na-channels-in-drg/2466 "2023-07-12T17:18:32Z")
To compensate or to not compensate during voltage clamp recordings of sodium channels in DRG neurons. I personally dont use it. I just keep a track on series resistance and keep 20% change acceptable. Whats your take. --- ## [Is there any developing, postnatal mouse brain scRNA-seq data available?](https://community.brain-map.org/t/is-there-any-developing-postnatal-mouse-brain-scrna-seq-data-available/2432)
**Author:** [@redbybeing](https://community.brain-map.org/u/redbybeing)\ **Replies:** 1\ **Last updated:** [July 1, 2023, 4:02pm UTC](https://community.brain-map.org/t/is-there-any-developing-postnatal-mouse-brain-scrna-seq-data-available/2432 "2023-07-01T16:02:46Z")
Hello, Does anyone know whether there is a developing, postnatal mouse brain scRNA-seq data available for download? I’ve been using Allen Mouse Whole Cortex and Hippocampus 10x data (adult) to annotate my scRNA-seq dat… --- ## [Neuron Population Density Amongst Regions (Stereology)](https://community.brain-map.org/t/neuron-population-density-amongst-regions-stereology/2404)
**Author:** [@cturner28](https://community.brain-map.org/u/cturner28)\ **Replies:** 0\ **Last updated:** [June 15, 2023, 7:27pm UTC](https://community.brain-map.org/t/neuron-population-density-amongst-regions-stereology/2404 "2023-06-15T19:27:27Z")
Hello, Are there raw counts/relative counts of neurons in different regions of the mouse brain. Density plots of types of neurons. Available in Allen? Thank you --- ## [I am specifically interested in the RNA-seq of the two human brains identified by H0351.2001 and H0351.2002. Are these datasets related to brain diseased or Normal persons?](https://community.brain-map.org/t/i-am-specifically-interested-in-the-rna-seq-of-the-two-human-brains-identified-by-h0351-2001-and-h0351-2002-are-these-datasets-related-to-brain-diseased-or-normal-persons/2351)
**Author:** [@Shahzaib](https://community.brain-map.org/u/Shahzaib)\ **Replies:** 1\ **Last updated:** [May 22, 2023, 3:49pm UTC](https://community.brain-map.org/t/i-am-specifically-interested-in-the-rna-seq-of-the-two-human-brains-identified-by-h0351-2001-and-h0351-2002-are-these-datasets-related-to-brain-diseased-or-normal-persons/2351 "2023-05-22T15:49:59Z")
Could you please provide a description of the RNA-seq datasets for the two human brains, H0351.2001 and H0351.2002? Additionally, I need to know if these datasets are related to brain diseased or normal individuals. --- ## [Testing a community proposal for OpenScope](https://community.brain-map.org/t/testing-a-community-proposal-for-openscope/2310)
**Author:** [@jerome](https://community.brain-map.org/u/jerome)\ **Replies:** 1\ **Last updated:** [April 21, 2023, 11:29pm UTC](https://community.brain-map.org/t/testing-a-community-proposal-for-openscope/2310 "2023-04-21T23:29:34Z")
Title: Investigating the Role of Interneuron Diversity in the Visual Cortex for Object Recognition and Visual Perception using OpenScope Introduction: The visual cortex plays a crucial role in processing and interpretin… --- ## [Signature of Hindbrain nuclei](https://community.brain-map.org/t/signature-of-hindbrain-nuclei/2236)
**Author:** [@JSchwamborn](https://community.brain-map.org/u/JSchwamborn)\ **Replies:** 4\ **Last updated:** [April 7, 2023, 4:00pm UTC](https://community.brain-map.org/t/signature-of-hindbrain-nuclei/2236 "2023-04-07T16:00:38Z")
Hi, We conducted single nuclei RNA-Seq of hindbrain organoids and now would like to use these data for further this analysis with the question if we could identify that certain cells belong to a particular region (nucle… --- ## [Interpolation method of the Average Template along the antero-posterior axis (from 100 µm to 10 µm)](https://community.brain-map.org/t/interpolation-method-of-the-average-template-along-the-antero-posterior-axis-from-100-m-to-10-m/2223)
**Author:** [@spiluso](https://community.brain-map.org/u/spiluso)\ **Replies:** 1\ **Last updated:** [March 13, 2023, 9:03pm UTC](https://community.brain-map.org/t/interpolation-method-of-the-average-template-along-the-antero-posterior-axis-from-100-m-to-10-m/2223 "2023-03-13T21:03:46Z")
Hello, In your paper from 2020 The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas, you mentioned that: We constructed an average template brain at 10 µm voxel resolution by interpolating high reso… --- ## [RS FS Cell Type Classification on Visual Coding Dataset](https://community.brain-map.org/t/rs-fs-cell-type-classification-on-visual-coding-dataset/2057)
**Author:** [@cr3000](https://community.brain-map.org/u/cr3000)\ **Replies:** 1\ **Last updated:** [January 3, 2023, 9:20pm UTC](https://community.brain-map.org/t/rs-fs-cell-type-classification-on-visual-coding-dataset/2057 "2023-01-03T21:20:39Z")
Hi everyone! I am a student currently interested in using the visual coding dataset to complete a class project on classifying regular spiking and fast spiking cells. Sorry if my question might not be the most well info… --- ## [Question about Quantifying Neuron Complexity with Sholl Analysis](https://community.brain-map.org/t/question-about-quantifying-neuron-complexity-with-sholl-analysis/1900)
**Author:** [@hsonoda24](https://community.brain-map.org/u/hsonoda24)\ **Replies:** 1\ **Last updated:** [October 21, 2022, 8:45pm UTC](https://community.brain-map.org/t/question-about-quantifying-neuron-complexity-with-sholl-analysis/1900 "2022-10-21T20:45:05Z")
Hello, my peers and I were wondering if dendrite and axon complexity can be accurately measured with Sholl analysis. Is it also possible to quantify neuron complexity with a single value through Sholl analysis? Thank you… --- ## [Comparing gene expression between two structures using log2(intensity) values](https://community.brain-map.org/t/comparing-gene-expression-between-two-structures-using-log2-intensity-values/1919)
**Author:** [@Carlos](https://community.brain-map.org/u/Carlos)\ **Replies:** 4\ **Last updated:** [October 21, 2022, 7:10pm UTC](https://community.brain-map.org/t/comparing-gene-expression-between-two-structures-using-log2-intensity-values/1919 "2022-10-21T19:10:06Z")
Hi all! I am new to this forum and to gene expression analysis, being this the first time I use data from the Allen Human Brain Atlas. I am trying to compare the expression of a particular gene (e.g. GRIN1) between two … --- ## [What is the format of gene expression value in allen human brain atlas?](https://community.brain-map.org/t/what-is-the-format-of-gene-expression-value-in-allen-human-brain-atlas/1830)
**Author:** [@jiwieli](https://community.brain-map.org/u/jiwieli)\ **Replies:** 1\ **Last updated:** [September 8, 2022, 3:29pm UTC](https://community.brain-map.org/t/what-is-the-format-of-gene-expression-value-in-allen-human-brain-atlas/1830 "2022-09-08T15:29:55Z")
hello, allen institute. I am fairly new to working with transcriptomics data. I download human brain data from Microarray Data Download :: Allen Brain Atlas: Human Brain. I want to do some differential gene expression a… --- ## [Theories on the synaptic algoritihm](https://community.brain-map.org/t/theories-on-the-synaptic-algoritihm/1727)
**Author:** [@7FQtekYfYfud7uxM2ZWu](https://community.brain-map.org/u/7FQtekYfYfud7uxM2ZWu)\ **Replies:** 0\ **Last updated:** [July 19, 2022, 9:36pm UTC](https://community.brain-map.org/t/theories-on-the-synaptic-algoritihm/1727 "2022-07-19T21:36:50Z")
hello does anyone know about any recent advances in cracking the synaptic algorithm? what are the current theories on this? to be clear by the synaptic algorithm I mean the rules that govern the phenomenon of where inp… --- ## [Questions on house keeping genes:](https://community.brain-map.org/t/questions-on-house-keeping-genes/1726)
**Author:** [@cjohnson23](https://community.brain-map.org/u/cjohnson23)\ **Replies:** 1\ **Last updated:** [July 18, 2022, 8:28pm UTC](https://community.brain-map.org/t/questions-on-house-keeping-genes/1726 "2022-07-18T20:28:41Z")
What are good house keeping genes to use with Patch-Seq? Should we be using housekeeping genes to normalize data? Can we use NormFinder to find good house keeping genes? https://moma.dk/normfinder-software --- ## [Question on Patch-seq data](https://community.brain-map.org/t/question-on-patch-seq-data/1724)
**Author:** [@cjohnson23](https://community.brain-map.org/u/cjohnson23)\ **Replies:** 3\ **Last updated:** [July 18, 2022, 7:44pm UTC](https://community.brain-map.org/t/question-on-patch-seq-data/1724 "2022-07-18T19:44:03Z")
We are looking at patch-seq transcriptomic data, do we need to a house keeping gene like GADPH to compare values of specific rna in different cells? --- ## [Is smart-seq matrix human multiple cortical areas normalized?](https://community.brain-map.org/t/is-smart-seq-matrix-human-multiple-cortical-areas-normalized/1703)
**Author:** [@StanDriessens](https://community.brain-map.org/u/StanDriessens)\ **Replies:** 1\ **Last updated:** [July 18, 2022, 3:36pm UTC](https://community.brain-map.org/t/is-smart-seq-matrix-human-multiple-cortical-areas-normalized/1703 "2022-07-18T15:36:25Z")
Hi, Can someone clarify if the counts in the smart-seq matrices for human cell types have been normalized (CPM)? If not is this dataset also available for normalized values? Thanks! Stan --- ## [Determination of the mouse LGN borders coordinates in order to reconstruct the whole LGN with its sub-structures (e.g., the individual layers)](https://community.brain-map.org/t/determination-of-the-mouse-lgn-borders-coordinates-in-order-to-reconstruct-the-whole-lgn-with-its-sub-structures-e-g-the-individual-layers/1688)
**Author:** [@Mostafa](https://community.brain-map.org/u/Mostafa)\ **Replies:** 4\ **Last updated:** [July 14, 2022, 10:38pm UTC](https://community.brain-map.org/t/determination-of-the-mouse-lgn-borders-coordinates-in-order-to-reconstruct-the-whole-lgn-with-its-sub-structures-e-g-the-individual-layers/1688 "2022-07-14T22:38:52Z")
Dear friends with alll due respect, I’m phD student and working on the Brain and eyes of the mouse. in a part of my thesis, I need to the coordinates of the whole LGN with its sub-structures (e.g., the individual layer… --- ## [3D representation of the mouse LGN and its sub-structures](https://community.brain-map.org/t/3d-representation-of-the-mouse-lgn-and-its-sub-structures/1692)
**Author:** [@Mostafa](https://community.brain-map.org/u/Mostafa)\ **Replies:** 2\ **Last updated:** [July 14, 2022, 10:31pm UTC](https://community.brain-map.org/t/3d-representation-of-the-mouse-lgn-and-its-sub-structures/1692 "2022-07-14T22:31:33Z")
Hello dear Friends Could you please help me in these cases and if possible send me their files or guide me how I can find them. 1) 3D representation of the mouse LGN and its sub-structures. 2) Mouse Brain Atlas. Than… --- ## [Control Human Brain Prefrontal Cortex snRNA-seq data](https://community.brain-map.org/t/control-human-brain-prefrontal-cortex-snrna-seq-data/1697)
**Author:** [@jet85](https://community.brain-map.org/u/jet85)\ **Replies:** 1\ **Last updated:** [June 30, 2022, 3:08pm UTC](https://community.brain-map.org/t/control-human-brain-prefrontal-cortex-snrna-seq-data/1697 "2022-06-30T15:08:33Z")
Hello I’m interested in collecting a control snRNA-seq dataset derived from human prefrontal cortex. Ideally, from non-neurologically impaired individuals, or even better from donors without any chronic illness. Also, i… --- ## [Width between brain sections](https://community.brain-map.org/t/width-between-brain-sections/1658)
**Author:** [@cgNeuro](https://community.brain-map.org/u/cgNeuro)\ **Replies:** 6\ **Last updated:** [June 22, 2022, 4:25pm UTC](https://community.brain-map.org/t/width-between-brain-sections/1658 "2022-06-22T16:25:02Z")
The developing mouse brain PND 14 atlas has 498 coronal images. Documentation regarding the atlas is that these sections are 25 µm thick. This would result in a brain that is 12.45 mm front to back. However, Paxinos a… --- ## [Scale bar measurements and pixel sizes of mouse brain images](https://community.brain-map.org/t/scale-bar-measurements-and-pixel-sizes-of-mouse-brain-images/1651)
**Author:** [@jishar](https://community.brain-map.org/u/jishar)\ **Replies:** 1\ **Last updated:** [June 21, 2022, 10:37pm UTC](https://community.brain-map.org/t/scale-bar-measurements-and-pixel-sizes-of-mouse-brain-images/1651 "2022-06-21T22:37:47Z")
Hello, I am working on a project which requires the use of images from the Allen Brain Atlas and their pixel sizes (micron/pixel). I have a few queries - In the URL mentioned above, the scale bar measure for the sam… --- ## [Some questions about Mouse Brain Atlas in Brain Explorer 2](https://community.brain-map.org/t/some-questions-about-mouse-brain-atlas-in-brain-explorer-2/1672)
**Author:** [@WThainan](https://community.brain-map.org/u/WThainan)\ **Replies:** 1\ **Last updated:** [June 21, 2022, 10:27pm UTC](https://community.brain-map.org/t/some-questions-about-mouse-brain-atlas-in-brain-explorer-2/1672 "2022-06-21T22:27:00Z")
I have some questions on Brain Explorer 2.I want to know what is the template of allen mouse brain atlas and how to define the structures in mouse brain? If have some documents or literatures that explain related issue… --- ## [Overlap Between Sections in Developing Mouse Brain Atlas](https://community.brain-map.org/t/overlap-between-sections-in-developing-mouse-brain-atlas/1662)
**Author:** [@cgNeuro](https://community.brain-map.org/u/cgNeuro)\ **Replies:** 4\ **Last updated:** [June 17, 2022, 11:26am UTC](https://community.brain-map.org/t/overlap-between-sections-in-developing-mouse-brain-atlas/1662 "2022-06-17T11:26:27Z")
The developing mouse brain atlas documentation says that the brain slices were cut at 20 µm thickness. The documentation also says that there were multiple animals used to create this atlas. My questions is, is there a… --- ## [How do you Interpret Gene Expression Values (counts)?](https://community.brain-map.org/t/how-do-you-interpret-gene-expression-values-counts/1639)
**Author:** [@AKHILAS](https://community.brain-map.org/u/AKHILAS)\ **Replies:** 2\ **Last updated:** [June 10, 2022, 3:53pm UTC](https://community.brain-map.org/t/how-do-you-interpret-gene-expression-values-counts/1639 "2022-06-10T15:53:42Z")
I am fairly new to working with transcriptomics data. I am analyzing the gene expression matrix from the Mouse Whole Cortex and Hippocampus SMART-seq data. I am wondering what the matrix value (count of intron and exons)… --- ## [How are the different electrophysiological sweeps for a single cell considered (e.g. taken into account or not), notably for the computation of I/O features?](https://community.brain-map.org/t/how-are-the-different-electrophysiological-sweeps-for-a-single-cell-considered-e-g-taken-into-account-or-not-notably-for-the-computation-of-i-o-features/1589)
**Author:** [@Jballbe](https://community.brain-map.org/u/Jballbe)\ **Replies:** 4\ **Last updated:** [April 28, 2022, 9:50am UTC](https://community.brain-map.org/t/how-are-the-different-electrophysiological-sweeps-for-a-single-cell-considered-e-g-taken-into-account-or-not-notably-for-the-computation-of-i-o-features/1589 "2022-04-28T09:50:35Z")
Hello everyone, I am interested into computing various electrophysiological features from the Allen Mouse cell type database, like the gain, the adaptation,… from scratch (i.e. from the spike-times and the stimulus trac… --- ## [Quantification of gene expression by in situ hybridization: finding and using the raw values](https://community.brain-map.org/t/quantification-of-gene-expression-by-in-situ-hybridization-finding-and-using-the-raw-values/153)
**Author:** [@brain](https://community.brain-map.org/u/brain)\ **Replies:** 31\ **Last updated:** [March 28, 2022, 1:11pm UTC](https://community.brain-map.org/t/quantification-of-gene-expression-by-in-situ-hybridization-finding-and-using-the-raw-values/153 "2022-03-28T13:11:38Z")
Many of the histological datasets that have been developed by the Allen Institute display gene expression by in situ hybridization (ISH), using colorimetric detection of RNA transcripts. Detailed methods describing how … --- ## [Z-score in Human Brain Atlas](https://community.brain-map.org/t/z-score-in-human-brain-atlas/1354)
**Author:** [@Tess](https://community.brain-map.org/u/Tess)\ **Replies:** 2\ **Last updated:** [February 16, 2022, 4:37pm UTC](https://community.brain-map.org/t/z-score-in-human-brain-atlas/1354 "2022-02-16T16:37:27Z")
Hello, I’m working with the allen human brain atlas gene search. I have already downloaded the expression data from the gene I’m researching (the DAOA gene). The thing I don’t understand is what the expression is compa… --- ## [Gabor stimuli properties](https://community.brain-map.org/t/gabor-stimuli-properties/1499)
**Author:** [@Mauro](https://community.brain-map.org/u/Mauro)\ **Replies:** 1\ **Last updated:** [February 25, 2022, 4:18am UTC](https://community.brain-map.org/t/gabor-stimuli-properties/1499 "2022-02-25T04:18:01Z")
Hi, the neuropixel dataset says the Gabor patches have a spatial frequency of 0.08 cycles per deg and a temporal frequency of 4 Hz. However the nature paper says it’s half those values. I wonder what are the actual value… --- ## [Do the MRI images match spatially with the resected tumor which cut into tissue blocks in Ivy GAP glioblastoma database?](https://community.brain-map.org/t/do-the-mri-images-match-spatially-with-the-resected-tumor-which-cut-into-tissue-blocks-in-ivy-gap-glioblastoma-database/954)
**Author:** [@QIN](https://community.brain-map.org/u/QIN)\ **Replies:** 4\ **Last updated:** [February 18, 2022, 2:30am UTC](https://community.brain-map.org/t/do-the-mri-images-match-spatially-with-the-resected-tumor-which-cut-into-tissue-blocks-in-ivy-gap-glioblastoma-database/954 "2022-02-18T02:30:19Z")
does anybody know that wether the MRI images of each patient’s glioblastoma match spatially with the resected tumor which cut into tissue blocks in Ivy GAP glioblastoma database?that is ,can we be able to find the corres… --- ## [Resources to Study Eye](https://community.brain-map.org/t/resources-to-study-eye/1417)
**Author:** [@rabi\_alkun](https://community.brain-map.org/u/rabi_alkun)\ **Replies:** 3\ **Last updated:** [January 31, 2022, 7:43am UTC](https://community.brain-map.org/t/resources-to-study-eye/1417 "2022-01-31T07:43:55Z")
Dear All, I watched the lecture series on Coding and VIsion 101 by Dr R. Clay Reid and Dr Chirstof Koch. I am interested in learning more. Can anyone suggest to me a place to learn more about the eye and other details of… --- ## [RNAseq data of the Brain Span Atlas of the Human Brain - confirmation of the method](https://community.brain-map.org/t/rnaseq-data-of-the-brain-span-atlas-of-the-human-brain-confirmation-of-the-method/1404)
**Author:** [@Macuchova](https://community.brain-map.org/u/Macuchova)\ **Replies:** 1\ **Last updated:** [January 6, 2022, 3:57pm UTC](https://community.brain-map.org/t/rnaseq-data-of-the-brain-span-atlas-of-the-human-brain-confirmation-of-the-method/1404 "2022-01-06T15:57:56Z")
Dear All, I have been annotating and analyzing the RNAseq data of the Brain Span Atlas of the Human Brain, downloaded from dbGaP under Study Accession: phs000755.v2.p1. Data, as saved in the SRA repository Studies : Br… [Previous page](https://community.brain-map.org/c/science/9.md?page=1) [Next page](https://community.brain-map.org/c/science/9.md?page=3)