# Science **URL:** https://community.brain-map.org/c/science/9.md [Latest](https://community.brain-map.org/latest.md) · [Categories](https://community.brain-map.org/categories.md) · [Tags](https://community.brain-map.org/tags.md) --- ## [About the Science category](https://community.brain-map.org/t/about-the-science-category/27)
**Author:** [@saskiad](https://community.brain-map.org/u/saskiad)\ **Replies:** 1\ **Last updated:** [February 11, 2023, 7:10pm UTC](https://community.brain-map.org/t/about-the-science-category/27 "2023-02-11T19:10:41Z")
A place for scientific questions and discussions about experimental methods, neuroscience, systems neurophysiology, sensory coding, behavior, or cell types of the brain. --- ## [Clarification of SEA-AD MTG layer-level IBA1–6E10 colocalization percentage](https://community.brain-map.org/t/clarification-of-sea-ad-mtg-layer-level-iba1-6e10-colocalization-percentage/5068)
**Author:** [@Alexy](https://community.brain-map.org/u/Alexy)\ **Replies:** 0\ **Last updated:** [September 5, 2026, 9:23pm UTC](https://community.brain-map.org/t/clarification-of-sea-ad-mtg-layer-level-iba1-6e10-colocalization-percentage/5068 "2026-09-05T21:23:09Z")
Hello SEA-AD team, I am preparing a donor-level secondary analysis using the publicly released June 2026 SEA-AD quantitative neuropathology summary and processed MTG endothelial pseudobulk data. I would appreciate clari… --- ## [Allen scSeq Dataset ](https://community.brain-map.org/t/allen-scseq-dataset/5044)
**Author:** [@BWalters](https://community.brain-map.org/u/BWalters)\ **Replies:** 1\ **Last updated:** [August 13, 2026, 5:36pm UTC](https://community.brain-map.org/t/allen-scseq-dataset/5044 "2026-08-13T17:36:50Z")
Hello, I am a graduate student in a circadian neuroscience lab and we have been using the single cell adult mouse brain public datasets for some preliminary/exploratory analyses. I was hoping to get some information abou… --- ## [Questions about Allen Mouse Brain Connectivity Atlas projection and injection data](https://community.brain-map.org/t/questions-about-allen-mouse-brain-connectivity-atlas-projection-and-injection-data/5000)
**Author:** [@omar341](https://community.brain-map.org/u/omar341)\ **Replies:** 1\ **Last updated:** [July 30, 2026, 5:38pm UTC](https://community.brain-map.org/t/questions-about-allen-mouse-brain-connectivity-atlas-projection-and-injection-data/5000 "2026-07-30T17:38:49Z")
Hi, I am a PhD student working on stochastic connectome-based modeling of pathological particle propagation in the mouse brain. I am using the Allen Mouse Brain Connectivity Atlas, especially the projection dataset from … --- ## [(SEA-AD) Donors and Samples](https://community.brain-map.org/t/sea-ad-donors-and-samples/4669)
**Author:** [@Victhagas](https://community.brain-map.org/u/Victhagas)\ **Replies:** 6\ **Last updated:** [July 26, 2026, 10:07pm UTC](https://community.brain-map.org/t/sea-ad-donors-and-samples/4669 "2026-07-26T22:07:05Z")
Hi guys, I was performing DEG analysis on the SEA-AD data and got confused about two things: When we access the AWS S3 Explorer, we can get the donor data, there are around 84 .h5ad files. I checked, and many of them… --- ## [Access to caudate nucleus snRNAseq data](https://community.brain-map.org/t/access-to-caudate-nucleus-snrnaseq-data/4990)
**Author:** [@lige8033](https://community.brain-map.org/u/lige8033)\ **Replies:** 1\ **Last updated:** [June 22, 2026, 7:31pm UTC](https://community.brain-map.org/t/access-to-caudate-nucleus-snrnaseq-data/4990 "2026-06-22T19:31:02Z")
Hi! I am interested in the single nuclei data from Kana et al (https://www.biorxiv.org/content/10.64898/2026.01.10.694705v2.full). As indicated in the paper, I tried to download the data via http link on AWS S3 Explorer … --- ## [Send me your worst meshes!](https://community.brain-map.org/t/send-me-your-worst-meshes/4962)
**Author:** [@scruffy](https://community.brain-map.org/u/scruffy)\ **Replies:** 1\ **Last updated:** [June 7, 2026, 7:47am UTC](https://community.brain-map.org/t/send-me-your-worst-meshes/4962 "2026-06-07T07:47:50Z")
Hi all, I have a tool that creates and fixes meshes. It can start from bad tracings and photographs. It works great for me, now I’d like to make sure it works for you too. If you’d like to link me to the worst of your so… --- ## [Iontophoretic AAV injections](https://community.brain-map.org/t/iontophoretic-aav-injections/4910)
**Author:** [@zeitgeber](https://community.brain-map.org/u/zeitgeber)\ **Replies:** 1\ **Last updated:** [June 5, 2026, 11:10pm UTC](https://community.brain-map.org/t/iontophoretic-aav-injections/4910 "2026-06-05T23:10:06Z")
Hey guys, I’m a postdoc who’s been using the Allen Institute’s protocol for iontophoretic injections of AAVs for some years now ( Stereotaxic Injection by Iontophoresis V.8 protocol abstract ). Great protocol, works ver… --- ## [Request for independent replication/falsification: reproducible in-silico + in-vivo EEG package for “Hallucinatory Domestication”](https://community.brain-map.org/t/request-for-independent-replication-falsification-reproducible-in-silico-in-vivo-eeg-package-for-hallucinatory-domestication/4860)
**Author:** [@Najih](https://community.brain-map.org/u/Najih)\ **Replies:** 1\ **Last updated:** [June 3, 2026, 4:06am UTC](https://community.brain-map.org/t/request-for-independent-replication-falsification-reproducible-in-silico-in-vivo-eeg-package-for-hallucinatory-domestication/4860 "2026-06-03T04:06:41Z")
Hello everyone, I’m Najih O. Salhab (independent interdisciplinary researcher). I’m sharing open, fully reproducible Zenodo packages (Jupyter notebooks + run instructions + exported outputs) and I would sincerely apprec… --- ## [Freezing of isolated nuclei](https://community.brain-map.org/t/freezing-of-isolated-nuclei/1081)
**Author:** [@Martina17](https://community.brain-map.org/u/Martina17)\ **Replies:** 2\ **Last updated:** [May 11, 2026, 1:54pm UTC](https://community.brain-map.org/t/freezing-of-isolated-nuclei/1081 "2026-05-11T13:54:26Z")
Hi, I am isolating nuclei from snap frozen brain tissue (prefrontal cortex). The nuclei are then used to perform single-nuclei RNA seq using 10x genomics technology. I normally extract the nuclei from the tissue and th… --- ## [Mouse and human embryonic brain scRNAseq web links/portal](https://community.brain-map.org/t/mouse-and-human-embryonic-brain-scrnaseq-web-links-portal/4890)
**Author:** [@Namlong](https://community.brain-map.org/u/Namlong)\ **Replies:** 1\ **Last updated:** [May 7, 2026, 11:02pm UTC](https://community.brain-map.org/t/mouse-and-human-embryonic-brain-scrnaseq-web-links-portal/4890 "2026-05-07T23:02:42Z")
Hi all, could you refer a web link or portal to check gene expression in different cell types in developing mouse brain (between E13.5-18.5) or fetal human brain. Any brain region is fine. But preferably in the neocortic… --- ## [How do some isocortex regions have such large ipsilateral connectivity?](https://community.brain-map.org/t/how-do-some-isocortex-regions-have-such-large-ipsilateral-connectivity/4870)
**Author:** [@mruge](https://community.brain-map.org/u/mruge)\ **Replies:** 1\ **Last updated:** [March 30, 2026, 3:36pm UTC](https://community.brain-map.org/t/how-do-some-isocortex-regions-have-such-large-ipsilateral-connectivity/4870 "2026-03-30T15:36:01Z")
I have been trying to create a computational model of the mouse isocortex using the connectivity matrix (Supplementary Table 3 from “A mesoscale connectome of the mouse brain” by Oh, S., Harris, J., Ng, L. et al.). I am … --- ## [Opposite z-score trends for different ADNP probes in Allen Human Brain Atlas – question about probe targets and reliability](https://community.brain-map.org/t/opposite-z-score-trends-for-different-adnp-probes-in-allen-human-brain-atlas-question-about-probe-targets-and-reliability/4837)
**Author:** [@Zirui](https://community.brain-map.org/u/Zirui)\ **Replies:** 2\ **Last updated:** [February 10, 2026, 7:53am UTC](https://community.brain-map.org/t/opposite-z-score-trends-for-different-adnp-probes-in-allen-human-brain-atlas-question-about-probe-targets-and-reliability/4837 "2026-02-10T07:53:04Z")
Hi all, I am analyzing ADNP expression in the Allen Human Brain Atlas (microarray dataset) and encountered a probe-level inconsistency that I would appreciate some guidance on. Specifically, ADNP is represented by mult… --- ## [Were neurons and non-neurons sequenced using the same protocol?](https://community.brain-map.org/t/were-neurons-and-non-neurons-sequenced-using-the-same-protocol/4845)
**Author:** [@noamiz](https://community.brain-map.org/u/noamiz)\ **Replies:** 1\ **Last updated:** [February 6, 2026, 9:58pm UTC](https://community.brain-map.org/t/were-neurons-and-non-neurons-sequenced-using-the-same-protocol/4845 "2026-02-06T21:58:29Z")
Hi, Quick question about the dataset: were neurons and non-neurons processed and sequenced using the exact same protocol (library prep, chemistry, sequencing, etc.), or were there any differences between them? asking b… --- ## [I am seeing a cluster in the query that is not alligning with ref (SEA-AD snRNAseq MTG)](https://community.brain-map.org/t/i-am-seeing-a-cluster-in-the-query-that-is-not-alligning-with-ref-sea-ad-snrnaseq-mtg/4781)
**Author:** [@ashaypatel](https://community.brain-map.org/u/ashaypatel)\ **Replies:** 5\ **Last updated:** [January 16, 2026, 10:30pm UTC](https://community.brain-map.org/t/i-am-seeing-a-cluster-in-the-query-that-is-not-alligning-with-ref-sea-ad-snrnaseq-mtg/4781 "2026-01-16T22:30:27Z")
Hello, I created a query data set using SEA-AD snRNAseq MTG data from the raw fastqs at sage Synape (with clinical consensus diagnosis of Alzheimers disease and Control). I ran cell ranger (with introns) and perfomed QC… --- ## [Questions about Chiari malformation, esp psychiatric manifestations of tonsillar ectopia/Chiari I malformation](https://community.brain-map.org/t/questions-about-chiari-malformation-esp-psychiatric-manifestations-of-tonsillar-ectopia-chiari-i-malformation/3638)
**Author:** [@Kelsey](https://community.brain-map.org/u/Kelsey)\ **Replies:** 1\ **Last updated:** [November 24, 2025, 10:33am UTC](https://community.brain-map.org/t/questions-about-chiari-malformation-esp-psychiatric-manifestations-of-tonsillar-ectopia-chiari-i-malformation/3638 "2025-11-24T10:33:45Z")
Hello, I am looking to learn more about the possible psychiatric (not felt) symptoms of a Chiari I malformation. There is very little easily accessible information about this, but one thing I’ve observed is that people … --- ## [Spatial Transcriptomics of MERFISH Data](https://community.brain-map.org/t/spatial-transcriptomics-of-merfish-data/4721)
**Author:** [@SKadar11](https://community.brain-map.org/u/SKadar11)\ **Replies:** 4\ **Last updated:** [October 29, 2025, 4:53pm UTC](https://community.brain-map.org/t/spatial-transcriptomics-of-merfish-data/4721 "2025-10-29T16:53:30Z")
Hello all, I am trying to investigate heterogeneity of a specific few genes in a specific region of the brain. However, looking at the metadata files, “gene” and “cell\_metadata” for the Zeng data, I do not see any categ… --- ## [Projection from basolateral amygdala to nucleus accumbens](https://community.brain-map.org/t/projection-from-basolateral-amygdala-to-nucleus-accumbens/4705)
**Author:** [@kristylmw](https://community.brain-map.org/u/kristylmw)\ **Replies:** 1\ **Last updated:** [October 14, 2025, 4:04am UTC](https://community.brain-map.org/t/projection-from-basolateral-amygdala-to-nucleus-accumbens/4705 "2025-10-14T04:04:38Z")
Dear community I am an Honours student working on rat brain circuits, ans I am trying to examine projections between the basolateral amygdala (BLA) and the nucleus accumbens (NAc). In the Allen mouse data, I did not obs… --- ## [SEA-AD BC Matrices Question](https://community.brain-map.org/t/sea-ad-bc-matrices-question/4696)
**Author:** [@eitan.kaplan](https://community.brain-map.org/u/eitan.kaplan)\ **Replies:** 0\ **Last updated:** [September 12, 2025, 8:27pm UTC](https://community.brain-map.org/t/sea-ad-bc-matrices-question/4696 "2025-09-12T20:27:16Z")
I am the Scientific Project Manager for the SEA-AD Consortium. I am posting a community question and answer received via email related to working with SEA-AD data: Q: “I want to work with your MTG snRNAseq data that is … --- ## [Left\_right\_ccf\_coordinate of the Visual Coding Neuropixels data](https://community.brain-map.org/t/left-right-ccf-coordinate-of-the-visual-coding-neuropixels-data/4649)
**Author:** [@NaixinRen](https://community.brain-map.org/u/NaixinRen)\ **Replies:** 7\ **Last updated:** [August 25, 2025, 1:53am UTC](https://community.brain-map.org/t/left-right-ccf-coordinate-of-the-visual-coding-neuropixels-data/4649 "2025-08-25T01:53:45Z")
Hi, I was trying to understand whether the recording sites of the visual coding neuropixels are in the left or the right hemisphere. I have noticed that in the technical whitepaper the monitor was placed at the mouse’s … --- ## [Registering partial 2D IHC images to Allen Brain Atlas using QuickNII](https://community.brain-map.org/t/registering-partial-2d-ihc-images-to-allen-brain-atlas-using-quicknii/4651)
**Author:** [@michelletytong](https://community.brain-map.org/u/michelletytong)\ **Replies:** 2\ **Last updated:** [August 16, 2025, 7:04pm UTC](https://community.brain-map.org/t/registering-partial-2d-ihc-images-to-allen-brain-atlas-using-quicknii/4651 "2025-08-16T19:04:27Z")
Hi all, I’m wondering if anyone else has successfully used QuickNII to register IHC images of specific brain regions to the Allen Brain Atlas. We have an IHC dataset of just the hippocampal formation, with 3-4 channels … --- ## [Anyone familiar with studies on consciousness in computational neuroscience?](https://community.brain-map.org/t/anyone-familiar-with-studies-on-consciousness-in-computational-neuroscience/4420)
**Author:** [@GitItD](https://community.brain-map.org/u/GitItD)\ **Replies:** 1\ **Last updated:** [May 27, 2025, 8:57pm UTC](https://community.brain-map.org/t/anyone-familiar-with-studies-on-consciousness-in-computational-neuroscience/4420 "2025-05-27T20:57:12Z")
Hello, I am a first year PhD student in computational biology, interested in diverging my research into computational neuroscience. Currently, I am interested in studies on consciousness in computational neuroscience/bio… --- ## [Differentiating ISH signals from background](https://community.brain-map.org/t/differentiating-ish-signals-from-background/2309)
**Author:** [@trmurphy39](https://community.brain-map.org/u/trmurphy39)\ **Replies:** 2\ **Last updated:** [April 21, 2025, 6:59am UTC](https://community.brain-map.org/t/differentiating-ish-signals-from-background/2309 "2025-04-21T06:59:46Z")
Hello, I have a rather elementary question on how to interpret the Allen Brain mouse ISH data. Since there was no counterstain used in these experiments, any visible chromogenic signals should presumably represent targe… --- ## [有什么好的方法，可以确定小鼠视觉皮层相对与小鼠的前囟的位置呢？](https://community.brain-map.org/t/topic/4331)
**Author:** [@caicai1010662](https://community.brain-map.org/u/caicai1010662)\ **Replies:** 1\ **Last updated:** [April 16, 2025, 5:55pm UTC](https://community.brain-map.org/t/topic/4331 "2025-04-16T17:55:49Z")
在我们的实验研究中，小鼠的视觉皮层是我们当下研究的重点，在一个二维平面上，有什么好的方法，可以确定，视觉皮层相对与前囟点的位置呢？ --- ## [Artificial Cerebrospinal Fluid Protocols Published in 2020](https://community.brain-map.org/t/artificial-cerebrospinal-fluid-protocols-published-in-2020/4219)
**Author:** [@RosalindWYZ42](https://community.brain-map.org/u/RosalindWYZ42)\ **Replies:** 5\ **Last updated:** [March 18, 2025, 10:03pm UTC](https://community.brain-map.org/t/artificial-cerebrospinal-fluid-protocols-published-in-2020/4219 "2025-03-18T22:03:43Z")
We have been using the method from Ting 2018 for aCSF solutions and recently found ACSF I-IX. I assume ACSF I, IV, and IX, correspond to perfusion/cutting/recovery, holding, and recording for mouse brain slices. These se… --- ## [Documentation on Addtional Reference Data](https://community.brain-map.org/t/documentation-on-addtional-reference-data/4244)
**Author:** [@karton](https://community.brain-map.org/u/karton)\ **Replies:** 1\ **Last updated:** [March 13, 2025, 5:17pm UTC](https://community.brain-map.org/t/documentation-on-addtional-reference-data/4244 "2025-03-13T17:17:30Z")
Hi, I’m looking for documentation on the Additional Reference Data for the Developing Mouse Brain. Specifically, I am trying to find the slice thickness and interval for the E16.5 coronal brain. Thanks! --- ## [Does the Institute study the properties of Microtubules?](https://community.brain-map.org/t/does-the-institute-study-the-properties-of-microtubules/4165)
**Author:** [@AlWayne](https://community.brain-map.org/u/AlWayne)\ **Replies:** 1\ **Last updated:** [February 21, 2025, 1:08am UTC](https://community.brain-map.org/t/does-the-institute-study-the-properties-of-microtubules/4165 "2025-02-21T01:08:16Z")
Microtubules according to Roger Penrose and Stuart Hammeroff exhibit certain quantum properties besides organizing neurons. Has there been any discussion about this in any of the forums or among scientists at the Institu… --- ## [Why The Edge of MEC and LEC different between Allen Atlas and Paxinos Stereotaxic Coordinates?](https://community.brain-map.org/t/why-the-edge-of-mec-and-lec-different-between-allen-atlas-and-paxinos-stereotaxic-coordinates/4136)
**Author:** [@Rick\_Yuuu](https://community.brain-map.org/u/Rick_Yuuu)\ **Replies:** 2\ **Last updated:** [February 18, 2025, 10:27am UTC](https://community.brain-map.org/t/why-the-edge-of-mec-and-lec-different-between-allen-atlas-and-paxinos-stereotaxic-coordinates/4136 "2025-02-18T10:27:24Z")
The sagittal atlas at about lateral 3.36 mm of Allen map and Paxinos is: The Dorsal part of MEC in Paxinos was attributed to LEC in Allen map. This really troubles my resarch, for we’re preparing for MEC imaging. W… --- ## [Microarray Data: Schizophrenia](https://community.brain-map.org/t/microarray-data-schizophrenia/4150)
**Author:** [@Pritesh96k](https://community.brain-map.org/u/Pritesh96k)\ **Replies:** 2\ **Last updated:** [February 18, 2025, 9:47am UTC](https://community.brain-map.org/t/microarray-data-schizophrenia/4150 "2025-02-18T09:47:57Z")
Is there any Microarray data available for Schizophrenia disorder? If there please provide me the link --- ## [Artificial Brain generation copycat from a normnal brain possible?](https://community.brain-map.org/t/artificial-brain-generation-copycat-from-a-normnal-brain-possible/4125)
**Author:** [@Wanderer11](https://community.brain-map.org/u/Wanderer11)\ **Replies:** 2\ **Last updated:** [February 7, 2025, 9:39am UTC](https://community.brain-map.org/t/artificial-brain-generation-copycat-from-a-normnal-brain-possible/4125 "2025-02-07T09:39:07Z")
Hello, everyone I’m new to this cite and I would like to know if artificial brains can be generated by coding a whole brain using the capabilities of AI? Or are we to far off from such advancements? Can we start for exa… [Next page](https://community.brain-map.org/c/science/9.md?page=1)