# Science **URL:** https://community.brain-map.org/c/science/9.md?page=1 [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:** 2 --- ## [Neurotransmitter type filter in MERFISH data](https://community.brain-map.org/t/neurotransmitter-type-filter-in-merfish-data/4073)
**Author:** [@IPS](https://community.brain-map.org/u/IPS)\ **Replies:** 2\ **Last updated:** [January 16, 2025, 9:55pm UTC](https://community.brain-map.org/t/neurotransmitter-type-filter-in-merfish-data/4073 "2025-01-16T21:55:15Z")
Hello! I am new exploring the Allen Brain Map resources, so maybe this is a silly question. Exploring the Spatial Transcriptomics database for mouse brain, I noticed that when filtering by neurotransmitter type and NA ,… --- ## [Phenotype of GCaMP6 (Ai148/Ai162) + Cre mouse lines](https://community.brain-map.org/t/phenotype-of-gcamp6-ai148-ai162-cre-mouse-lines/4045)
**Author:** [@mthunemann](https://community.brain-map.org/u/mthunemann)\ **Replies:** 3\ **Last updated:** [January 13, 2025, 10:35pm UTC](https://community.brain-map.org/t/phenotype-of-gcamp6-ai148-ai162-cre-mouse-lines/4045 "2025-01-13T22:35:49Z")
Dear Community, we want to express GCaMP6s or 6f in Layer 5 pyramidal neurons. We use the Rbp4-Cre\_KL100 line and see delayed growth (postnatally) in Ai148 x Cre mice, but Ai162 x Cre mice seem to be fine. Mice have abo… --- ## [Are raw intracellular recording potential traces compensated for offset potential?](https://community.brain-map.org/t/are-raw-intracellular-recording-potential-traces-compensated-for-offset-potential/3854)
**Author:** [@Jballbe](https://community.brain-map.org/u/Jballbe)\ **Replies:** 1\ **Last updated:** [November 20, 2024, 4:53pm UTC](https://community.brain-map.org/t/are-raw-intracellular-recording-potential-traces-compensated-for-offset-potential/3854 "2024-11-20T16:53:23Z")
Hi, I am analyzing the raw traces of intracellular recordings. I noticed that in the Gouwens et al 2019 paper, it is mentioned : Data were reported uncorrected for the measured –14 mV liquid junction potential between… --- ## [Mouse spinal cord reference atlas: How to get stacks and vector graphics for registration](https://community.brain-map.org/t/mouse-spinal-cord-reference-atlas-how-to-get-stacks-and-vector-graphics-for-registration/3088)
**Author:** [@sulli419](https://community.brain-map.org/u/sulli419)\ **Replies:** 11\ **Last updated:** [September 5, 2024, 8:26am UTC](https://community.brain-map.org/t/mouse-spinal-cord-reference-atlas-how-to-get-stacks-and-vector-graphics-for-registration/3088 "2024-09-05T08:26:48Z")
Hello, I want to use the Allen adult mouse spinal cord atlas to register my spinal images. I would like to get a stack of all the outlined/drawn images (atlas with all labels removed). Is this available to download an… --- ## [Is there documentation for neuropil trace calculation? Visual Coding 2P](https://community.brain-map.org/t/is-there-documentation-for-neuropil-trace-calculation-visual-coding-2p/3585)
**Author:** [@nas225](https://community.brain-map.org/u/nas225)\ **Replies:** 2\ **Last updated:** [September 4, 2024, 12:25am UTC](https://community.brain-map.org/t/is-there-documentation-for-neuropil-trace-calculation-visual-coding-2p/3585 "2024-09-04T00:25:53Z")
Hi everyone, I’m working with the Visual Coding 2P data, and I’m interested in understanding what methods and calculations were used to derive the provided neuropil traces. So far, I haven’t been able to find any detail… --- ## [Relocate human's all cells](https://community.brain-map.org/t/relocate-humans-all-cells/3609)
**Author:** [@somnathdashs](https://community.brain-map.org/u/somnathdashs)\ **Replies:** 0\ **Last updated:** [August 25, 2024, 5:52pm UTC](https://community.brain-map.org/t/relocate-humans-all-cells/3609 "2024-08-25T17:52:51Z")
What happens if we create a way to relocate all the human cell (of a person) one by one to another place and to readjust them in a right away also those cells were alive then, what will happens would he will in same cons… --- ## [Why child atlas not proving good results for its age, but other are working well for me on same data?](https://community.brain-map.org/t/why-child-atlas-not-proving-good-results-for-its-age-but-other-are-working-well-for-me-on-same-data/3539)
**Author:** [@huma](https://community.brain-map.org/u/huma)\ **Replies:** 0\ **Last updated:** [July 30, 2024, 7:22am UTC](https://community.brain-map.org/t/why-child-atlas-not-proving-good-results-for-its-age-but-other-are-working-well-for-me-on-same-data/3539 "2024-07-30T07:22:49Z")
I am using multiple atlases to check their development per age, all atlases are working well only one is giving wrong result, though its made for 8-12 years but give result for 20 onward. --- ## [Astrocyte subtypes](https://community.brain-map.org/t/astrocyte-subtypes/3378)
**Author:** [@Harker](https://community.brain-map.org/u/Harker)\ **Replies:** 3\ **Last updated:** [July 24, 2024, 12:00pm UTC](https://community.brain-map.org/t/astrocyte-subtypes/3378 "2024-07-24T12:00:46Z")
I’m a neuropathologist at the DoD/USU Brain Tissue repository studying the neuropathology of blast-associated mTBI. Blast-exposed service members, especially those in the Special Forces, sometimes develop a neuropsychiat… --- ## [Would like to volunteer](https://community.brain-map.org/t/would-like-to-volunteer/3474)
**Author:** [@Alex1](https://community.brain-map.org/u/Alex1)\ **Replies:** 0\ **Last updated:** [July 11, 2024, 1:21pm UTC](https://community.brain-map.org/t/would-like-to-volunteer/3474 "2024-07-11T13:21:32Z")
I am a biologist and would like to participate in a brain mapping project. I have experience with proofreading in CAVE. Does anyone here know of opportunities to be involved at the Allen Institute? --- ## [Is there another term for "frontal marginal gyrus"](https://community.brain-map.org/t/is-there-another-term-for-frontal-marginal-gyrus/3430)
**Author:** [@sabrawer](https://community.brain-map.org/u/sabrawer)\ **Replies:** 3\ **Last updated:** [July 3, 2024, 3:05pm UTC](https://community.brain-map.org/t/is-there-another-term-for-frontal-marginal-gyrus/3430 "2024-07-03T15:05:04Z")
In the interactive atlas of human adult, gyrus view, there is an area marked “frontal marginal gyrus” (2nd and 3rd sections.). There are very few online references to this term (via google). Is there another name (or se… --- ## [Single Neuron Theory Of Consciousness](https://community.brain-map.org/t/single-neuron-theory-of-consciousness/1100)
**Author:** [@Cameron](https://community.brain-map.org/u/Cameron)\ **Replies:** 9\ **Last updated:** [July 17, 2022, 2:49am UTC](https://community.brain-map.org/t/single-neuron-theory-of-consciousness/1100 "2022-07-17T02:49:29Z")
Hello, Senior at Port Townsend High School in Washington State here. I’ve been reading up a bit on theories on consciousness, and I’ve come across a couple that worry me, hoping to get a neuroscientist’s take on this. I… --- ## [SEA-AD snATAC-seq data](https://community.brain-map.org/t/sea-ad-snatac-seq-data/2776)
**Author:** [@eitan.kaplan](https://community.brain-map.org/u/eitan.kaplan)\ **Replies:** 4\ **Last updated:** [April 22, 2024, 1:06pm UTC](https://community.brain-map.org/t/sea-ad-snatac-seq-data/2776 "2024-04-22T13:06:57Z")
I am the Scientific Project Manager for the SEA-AD Consortium. I am posting a community question received via email related to working with SEA-AD data: I am interested in using the SEA-AD dataset. I was wondering if yo… --- ## [The time of the circadian time points in the mouse brain scRNAseq dataset](https://community.brain-map.org/t/the-time-of-the-circadian-time-points-in-the-mouse-brain-scrnaseq-dataset/3252)
**Author:** [@kayihui](https://community.brain-map.org/u/kayihui)\ **Replies:** 0\ **Last updated:** [April 11, 2024, 9:58am UTC](https://community.brain-map.org/t/the-time-of-the-circadian-time-points-in-the-mouse-brain-scrnaseq-dataset/3252 "2024-04-11T09:58:30Z")
Hello, First of all, thank you for providing this wonder resources and including light/dark time points for us to study the circadian changes of gene expression in the brain. I’d like to have a little bit more details … --- ## [Call for participants from the neuroimaging community - WasON study](https://community.brain-map.org/t/call-for-participants-from-the-neuroimaging-community-wason-study/3236)
**Author:** [@davide\_coraci](https://community.brain-map.org/u/davide_coraci)\ **Replies:** 0\ **Last updated:** [April 5, 2024, 5:36pm UTC](https://community.brain-map.org/t/call-for-participants-from-the-neuroimaging-community-wason-study/3236 "2024-04-05T17:36:18Z")
Dear all, We are recruiting participants worldwide and it would be fantastic if you could take part in the WasON study. The aim of the study is to investigate how neuroscientists and researchers with some familiarity w… --- ## [How to do a correlation analysis between two specific genes across different tissues](https://community.brain-map.org/t/how-to-do-a-correlation-analysis-between-two-specific-genes-across-different-tissues/3193)
**Author:** [@MNani](https://community.brain-map.org/u/MNani)\ **Replies:** 5\ **Last updated:** [April 3, 2024, 5:23pm UTC](https://community.brain-map.org/t/how-to-do-a-correlation-analysis-between-two-specific-genes-across-different-tissues/3193 "2024-04-03T17:23:16Z")
Hey everyone! I am new to the forum and It’s my first time using the Allen mouse brain atlas. I am looking to do an analysis where for each mice within the dataset I would need to extract the data (ISH or 10x) for the e… --- ## [Interpreting Graphs in SEA-AD Gene Expression Trajectory Viewer and Comparative Viewer](https://community.brain-map.org/t/interpreting-graphs-in-sea-ad-gene-expression-trajectory-viewer-and-comparative-viewer/3126)
**Author:** [@eitan.kaplan](https://community.brain-map.org/u/eitan.kaplan)\ **Replies:** 1\ **Last updated:** [March 6, 2024, 5:25pm UTC](https://community.brain-map.org/t/interpreting-graphs-in-sea-ad-gene-expression-trajectory-viewer-and-comparative-viewer/3126 "2024-03-06T17:25:44Z")
I am the Scientific Project Manager for the SEA-AD Consortium. I am posting a community question received via email related to working with SEA-AD data: I have recently started browsing your fantastic dataset on the SEA… --- ## [Question about data in AGEA](https://community.brain-map.org/t/question-about-data-in-agea/2952)
**Author:** [@G.SZ](https://community.brain-map.org/u/G.SZ)\ **Replies:** 4\ **Last updated:** [March 4, 2024, 7:16am UTC](https://community.brain-map.org/t/question-about-data-in-agea/2952 "2024-03-04T07:16:37Z")
Hi, I have a question about AGEA. Does the data in AGEA go through registration？ If I select a gene, like Wfs1, getting into its page which shows its contents like this: Experiment Detail :: Allen Brain Atlas: Mouse B… --- ## [Animal numbers in connectivity map](https://community.brain-map.org/t/animal-numbers-in-connectivity-map/3093)
**Author:** [@R91](https://community.brain-map.org/u/R91)\ **Replies:** 0\ **Last updated:** [February 20, 2024, 2:27pm UTC](https://community.brain-map.org/t/animal-numbers-in-connectivity-map/3093 "2024-02-20T14:27:57Z")
Hi, The Oh et al. (2014) Nature paper reported Phase 1 (469) brains in the experimental procedure. I was wondering how many brains were used in Phase 2 and what is the reference for this? I am specifically looking at Hc… --- ## [Normalized MNI or Talaraich coordinates for modified Brodmann areas](https://community.brain-map.org/t/normalized-mni-or-talaraich-coordinates-for-modified-brodmann-areas/3059)
**Author:** [@shennan](https://community.brain-map.org/u/shennan)\ **Replies:** 0\ **Last updated:** [February 6, 2024, 2:38pm UTC](https://community.brain-map.org/t/normalized-mni-or-talaraich-coordinates-for-modified-brodmann-areas/3059 "2024-02-06T14:38:56Z")
Hello, I would like to use the Allen Brain Atlas - MRI Donor Data - Human Brain - MRI to find the normalized MNI or Talaraich coordinates of Modified Brodmann areas. In particular, subregions of Brodmann Area 40. When I… --- ## [How do I get the MIN coordinate of the mRNA express cortex in the Aging, Dementia, and TBI study](https://community.brain-map.org/t/how-do-i-get-the-min-coordinate-of-the-mrna-express-cortex-in-the-aging-dementia-and-tbi-study/2946)
**Author:** [@alienx-zero](https://community.brain-map.org/u/alienx-zero)\ **Replies:** 2\ **Last updated:** [January 25, 2024, 5:05pm UTC](https://community.brain-map.org/t/how-do-i-get-the-min-coordinate-of-the-mrna-express-cortex-in-the-aging-dementia-and-tbi-study/2946 "2024-01-25T17:05:58Z")
Hi, Recently, I would like to use the mRNA expression information to analyze AD. I have downloaded the gene expression table here Data Download :: Allen Brain Atlas: Aging, Dementia and TBI Study. However, it only provid… --- ## [Questions about RNA seq SEA-AD data](https://community.brain-map.org/t/questions-about-rna-seq-sea-ad-data/2662)
**Author:** [@eitan.kaplan](https://community.brain-map.org/u/eitan.kaplan)\ **Replies:** 9\ **Last updated:** [December 12, 2023, 7:40am UTC](https://community.brain-map.org/t/questions-about-rna-seq-sea-ad-data/2662 "2023-12-12T07:40:26Z")
I am the Scientific Project Manager for the SEA-AD Consortium. I am posting a community question received via email related to working with SEA-AD data: We have been trying to work with SEA-AD data for some time, includ… --- ## [Layer-wise differences in Mouse Reference Atlas Entorhinal Area vs Isocortex](https://community.brain-map.org/t/layer-wise-differences-in-mouse-reference-atlas-entorhinal-area-vs-isocortex/2747)
**Author:** [@mreko](https://community.brain-map.org/u/mreko)\ **Replies:** 0\ **Last updated:** [December 4, 2023, 2:51pm UTC](https://community.brain-map.org/t/layer-wise-differences-in-mouse-reference-atlas-entorhinal-area-vs-isocortex/2747 "2023-12-04T14:51:16Z")
I was trying to understand the reasoning behind layer annotations in lateral and medial Entorhinal Area compared to isocortex. I have read that initial differentiation between these regions were based on the calbindin ex… --- ## [SEA-AD Datasets Query](https://community.brain-map.org/t/sea-ad-datasets-query/2670)
**Author:** [@eitan.kaplan](https://community.brain-map.org/u/eitan.kaplan)\ **Replies:** 1\ **Last updated:** [October 26, 2023, 4:56pm UTC](https://community.brain-map.org/t/sea-ad-datasets-query/2670 "2023-10-26T16:56:31Z")
I am the Scientific Project Manager for the SEA-AD Consortium. I am posting a community question received via email related to working with SEA-AD data: I have made use of some of the SEA-AD Allen Institute Datasets for… --- ## [Can the transcriptomics data be used to estimate the density of different cell types across regions](https://community.brain-map.org/t/can-the-transcriptomics-data-be-used-to-estimate-the-density-of-different-cell-types-across-regions/2648)
**Author:** [@Timo](https://community.brain-map.org/u/Timo)\ **Replies:** 8\ **Last updated:** [October 20, 2023, 7:53pm UTC](https://community.brain-map.org/t/can-the-transcriptomics-data-be-used-to-estimate-the-density-of-different-cell-types-across-regions/2648 "2023-10-20T19:53:01Z")
Hi, First, I have a very naive / basic question about the way that transcriptomics data can be used. Would it be possible to use it to plot the density of cell types across brain areas? (Similar to what you can do with … --- ## [Presenting your stimuli in my own experiments](https://community.brain-map.org/t/presenting-your-stimuli-in-my-own-experiments/2590)
**Author:** [@danielpollak](https://community.brain-map.org/u/danielpollak)\ **Replies:** 2\ **Last updated:** [October 10, 2023, 6:04pm UTC](https://community.brain-map.org/t/presenting-your-stimuli-in-my-own-experiments/2590 "2023-10-10T18:04:41Z")
Hello, I’m trying to present your locally sparse noise stimulus with warping to an animal in a new experiment, as is produced from this line of code from https://alleninstitute.github.io/AllenSDK/\_static/examples/nb/br… --- ## [WGCNA analysis of microarray data from H0351.2001](https://community.brain-map.org/t/wgcna-analysis-of-microarray-data-from-h0351-2001/2544)
**Author:** [@Libra66](https://community.brain-map.org/u/Libra66)\ **Replies:** 2\ **Last updated:** [August 18, 2023, 3:52pm UTC](https://community.brain-map.org/t/wgcna-analysis-of-microarray-data-from-h0351-2001/2544 "2023-08-18T15:52:25Z")
Hi, I found this WGCNA analysis of microarray data from one person H0351.2001 http://api.brain-map.org/examples/wgcna/index.html I am wondering how representative the analysis is and if there is any chance to integrat… --- ## [Noise with Neuropixels](https://community.brain-map.org/t/noise-with-neuropixels/2537)
**Author:** [@lena.g3](https://community.brain-map.org/u/lena.g3)\ **Replies:** 3\ **Last updated:** [August 9, 2023, 11:29pm UTC](https://community.brain-map.org/t/noise-with-neuropixels/2537 "2023-08-09T23:29:00Z")
Hi there, I normally record from both mouse brain hemispheres (dorsomedial and dorsolateral striatum) and have noticed that when my ground pin (closer to the cerebellum) is on the same hemisphere as the electrophysiolog… --- ## [Dynamic Weight Motions in Modern AI](https://community.brain-map.org/t/dynamic-weight-motions-in-modern-ai/2533)
**Author:** [@LiveBacteria](https://community.brain-map.org/u/LiveBacteria)\ **Replies:** 1\ **Last updated:** [August 3, 2023, 11:07pm UTC](https://community.brain-map.org/t/dynamic-weight-motions-in-modern-ai/2533 "2023-08-03T23:07:49Z")
Hello all, Has the concept of dynamic motions applied to the weights of a neural network been explored? Short and simple. Thank you for your time, Tyler --- ## [Mouse Durotomy Surgery Tool](https://community.brain-map.org/t/mouse-durotomy-surgery-tool/2497)
**Author:** [@lena.g3](https://community.brain-map.org/u/lena.g3)\ **Replies:** 1\ **Last updated:** [July 17, 2023, 5:57pm UTC](https://community.brain-map.org/t/mouse-durotomy-surgery-tool/2497 "2023-07-17T17:57:40Z")
Hi there, I normally perform a craniotomy 5 days prior to Neuropixels probe insertion (to allow for 5 days post-surgery recovery) but I still see dura regrowth. So my question is: what surgery tool do you use for a duro… --- ## [Does anybody use a preheated syringe for injecting an agarose mixture during insertion of a Neuropixels probe?](https://community.brain-map.org/t/does-anybody-use-a-preheated-syringe-for-injecting-an-agarose-mixture-during-insertion-of-a-neuropixels-probe/2436)
**Author:** [@lena.g3](https://community.brain-map.org/u/lena.g3)\ **Replies:** 3\ **Last updated:** [July 16, 2023, 11:47pm UTC](https://community.brain-map.org/t/does-anybody-use-a-preheated-syringe-for-injecting-an-agarose-mixture-during-insertion-of-a-neuropixels-probe/2436 "2023-07-16T23:47:09Z")
Hi there, I inject agarose mixture into my cranial window to carefully insert a Neuropixels probe into my brain region of interest. I was wondering if anyone uses a preheated syringe for this? Best, Selena [Previous page](https://community.brain-map.org/c/science/9.md) [Next page](https://community.brain-map.org/c/science/9.md?page=2)