# \#experiment-design **URL:** https://community.brain-map.org/tag/experiment-design/37.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) --- ## [Missing R2 FASTQ files for Patch-seq dataset](https://community.brain-map.org/t/missing-r2-fastq-files-for-patch-seq-dataset/4852)
**Author:** [@nuo\_xu](https://community.brain-map.org/u/nuo_xu)\ **Replies:** 1\ **Last updated:** [April 8, 2026, 3:01am UTC](https://community.brain-map.org/t/missing-r2-fastq-files-for-patch-seq-dataset/4852 "2026-04-08T03:01:07Z")
Hello, The methods section in the paper “Connecting single-cell transcriptomes to projectomes in mouse visual cortex" states that libraries were sequenced as “fifty-base-pair paired-end reads.” However, when downloading… --- ## [Is there a universal code scheme for visual stimulation on the display](https://community.brain-map.org/t/is-there-a-universal-code-scheme-for-visual-stimulation-on-the-display/4487)
**Author:** [@caicai1010662](https://community.brain-map.org/u/caicai1010662)\ **Replies:** 1\ **Last updated:** [June 30, 2025, 7:25pm UTC](https://community.brain-map.org/t/is-there-a-universal-code-scheme-for-visual-stimulation-on-the-display/4487 "2025-06-30T19:25:01Z")
Recently, we will do visual stimulation experiments on mice, but we do not have the basis for doing such experiments. We have prepared a dedicated display screen, but we lack a visual stimulation for testing. Is there a … --- ## [Accessing frames for natural\_movie\_shuffled in Neuropixel data](https://community.brain-map.org/t/accessing-frames-for-natural-movie-shuffled-in-neuropixel-data/1010)
**Author:** [@cspurandare](https://community.brain-map.org/u/cspurandare)\ **Replies:** 23\ **Last updated:** [February 11, 2025, 12:44am UTC](https://community.brain-map.org/t/accessing-frames-for-natural-movie-shuffled-in-neuropixel-data/1010 "2025-02-11T00:44:56Z")
Hello, I am working with the Neuropixel data, and the “Functional Connectivity” experiment paradigm. In that, there is a block of 10 minutes, where the “natural\_movie\_shuffled” is presented. I was curious about how th… --- ## [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… --- ## [How can I optimize my snRNA-seq workflow—both experimentally and bioinformatically—to enable high-resolution transcriptomic cell type mapping?](https://community.brain-map.org/t/how-can-i-optimize-my-snrna-seq-workflow-both-experimentally-and-bioinformatically-to-enable-high-resolution-transcriptomic-cell-type-mapping/3902)
**Author:** [@sbhamidipati](https://community.brain-map.org/u/sbhamidipati)\ **Replies:** 2\ **Last updated:** [December 4, 2024, 6:21pm UTC](https://community.brain-map.org/t/how-can-i-optimize-my-snrna-seq-workflow-both-experimentally-and-bioinformatically-to-enable-high-resolution-transcriptomic-cell-type-mapping/3902 "2024-12-04T18:21:39Z")
Hello! I’m writing to get some guidance on optimizing my snRNA-seq workflow to facilitate accurate mapping to the Allen Institute’s transcriptomic types at the highest granularity possible. Specifically, Is there 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… --- ## [The meaning of some conditions in stimulus\_table in the VisualCodingNeuropixels project](https://community.brain-map.org/t/the-meaning-of-some-conditions-in-stimulus-table-in-the-visualcodingneuropixels-project/3440)
**Author:** [@weiwei2027](https://community.brain-map.org/u/weiwei2027)\ **Replies:** 4\ **Last updated:** [July 10, 2024, 5:05am UTC](https://community.brain-map.org/t/the-meaning-of-some-conditions-in-stimulus-table-in-the-visualcodingneuropixels-project/3440 "2024-07-10T05:05:44Z")
Hi, thank you very much for your work on VisualCodingNeuropixels and making it open access, which is very valuable in promoting research in this area. When I access this data using allensdk, there are a few conditions t… --- ## [Reproducing stimulation in Multimodal Characterization in Mouse Visual Cortex](https://community.brain-map.org/t/reproducing-stimulation-in-multimodal-characterization-in-mouse-visual-cortex/3279)
**Author:** [@deanpospisil](https://community.brain-map.org/u/deanpospisil)\ **Replies:** 2\ **Last updated:** [May 1, 2024, 4:37pm UTC](https://community.brain-map.org/t/reproducing-stimulation-in-multimodal-characterization-in-mouse-visual-cortex/3279 "2024-05-01T16:37:14Z")
Apologies if I have not been able to search hard enough but I have not been able to figure out exactly how to reproduce the current wave forms from the ephys characterization of the 4k neurons from their NWB files. Ther… --- ## [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 … --- ## [What is the meaning of atlas\_id and st\_level in 1.json?](https://community.brain-map.org/t/what-is-the-meaning-of-atlas-id-and-st-level-in-1-json/895)
**Author:** [@lguyot](https://community.brain-map.org/u/lguyot)\ **Replies:** 5\ **Last updated:** [December 4, 2023, 4:40am UTC](https://community.brain-map.org/t/what-is-the-meaning-of-atlas-id-and-st-level-in-1-json/895 "2023-12-04T04:40:16Z")
Dear forum users, A node in the hierarchy tree of the AIBS Mouse P56 1.json file looks like this: { "id": 68, "atlas\_id": 998, "ontology\_id": 1, … --- ## [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… --- ## [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 --- ## [New signaling mechanism in catecholaminergic neurons](https://community.brain-map.org/t/new-signaling-mechanism-in-catecholaminergic-neurons/2507)
**Author:** [@crourk](https://community.brain-map.org/u/crourk)\ **Replies:** 14\ **Last updated:** [August 3, 2023, 7:31am UTC](https://community.brain-map.org/t/new-signaling-mechanism-in-catecholaminergic-neurons/2507 "2023-08-03T07:31:42Z")
Ferritin has electrical properties that make it both useful in engineered electronic components and intriguing with its presence in the mammalian brain. A novel function of biological ferritin has been proposed for neura… --- ## [What is the OpenScope community proposal track?](https://community.brain-map.org/t/what-is-the-openscope-community-proposal-track/2409)
**Author:** [@jerome](https://community.brain-map.org/u/jerome)\ **Replies:** 1\ **Last updated:** [June 21, 2023, 4:40am UTC](https://community.brain-map.org/t/what-is-the-openscope-community-proposal-track/2409 "2023-06-21T04:40:45Z")
The OpenScope project has two aims: to establish a sustainable open-access platform and to foster a community of researchers around it. To achieve this goal, we need to solicit ideas for experimental proposals in a way t… --- ## [Tracer connectivity data between different layers available for the mouse brain?](https://community.brain-map.org/t/tracer-connectivity-data-between-different-layers-available-for-the-mouse-brain/100)
**Author:** [@g.rabuffo](https://community.brain-map.org/u/g.rabuffo)\ **Replies:** 2\ **Last updated:** [May 15, 2023, 10:04am UTC](https://community.brain-map.org/t/tracer-connectivity-data-between-different-layers-available-for-the-mouse-brain/100 "2023-05-15T10:04:17Z")
Hi! Is the tracer connectivity data between different layers available for the mouse brain? In particular I would need the connectivity information of the layers of the Entorhinal cortex. Apparently, afferent and effer… --- ## [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 … --- ## [Activity state of segmented neurons in Allen SDK datasets](https://community.brain-map.org/t/activity-state-of-segmented-neurons-in-allen-sdk-datasets/1644)
**Author:** [@nruffini](https://community.brain-map.org/u/nruffini)\ **Replies:** 4\ **Last updated:** [June 4, 2022, 4:02pm UTC](https://community.brain-map.org/t/activity-state-of-segmented-neurons-in-allen-sdk-datasets/1644 "2022-06-04T16:02:24Z")
Dear Community, I am working with the following three datasets: Visual behavior Optical Physiology, Visual Coding- Optical Physiology and Visual Behavior Neuropixels. I wondered if the segmentation of the neurons can … --- ## [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… --- ## [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… --- ## [How can I access the natural images used in the Brain Observatory?](https://community.brain-map.org/t/how-can-i-access-the-natural-images-used-in-the-brain-observatory/32)
**Author:** [@justin](https://community.brain-map.org/u/justin)\ **Replies:** 3\ **Last updated:** [August 4, 2021, 8:24pm UTC](https://community.brain-map.org/t/how-can-i-access-the-natural-images-used-in-the-brain-observatory/32 "2021-08-04T20:24:11Z")
Each of the experiments contains the images (or info necessary to reconstruct them). This Jupyter notebook demonstrates how to use the allensdk Python package to get or reconstruct each image: http://alleninstitute.git… --- ## [Visual behaviour and 2P data set rewards](https://community.brain-map.org/t/visual-behaviour-and-2p-data-set-rewards/1199)
**Author:** [@Tristan.j.philippe](https://community.brain-map.org/u/Tristan.j.philippe)\ **Replies:** 1\ **Last updated:** [July 22, 2021, 1:58am UTC](https://community.brain-map.org/t/visual-behaviour-and-2p-data-set-rewards/1199 "2021-07-22T01:58:47Z")
Hi, I would like to get whether an animal was rewarded or not per image presentation from the SDK datasets but cannot find it. There is a ‘insertsession’.rewards file but it’s of length 70 instead of ~4400 or the number… --- ## [Pixel size of mouse brain images in Allen Brain Atlas](https://community.brain-map.org/t/pixel-size-of-mouse-brain-images-in-allen-brain-atlas/1187)
**Author:** [@jishar](https://community.brain-map.org/u/jishar)\ **Replies:** 4\ **Last updated:** [July 19, 2021, 7:25pm UTC](https://community.brain-map.org/t/pixel-size-of-mouse-brain-images-in-allen-brain-atlas/1187 "2021-07-19T19:25:28Z")
Hello! I am working on a project related to spatio-molecular methods and for that, I’d need to know the pixel size (i.e. which real world length one pixel represents) of the images present in the URL below: https://mou… --- ## [Tracking mouse gaze on screen clarifications](https://community.brain-map.org/t/tracking-mouse-gaze-on-screen-clarifications/1103)
**Author:** [@Pete](https://community.brain-map.org/u/Pete)\ **Replies:** 2\ **Last updated:** [June 2, 2021, 12:03am UTC](https://community.brain-map.org/t/tracking-mouse-gaze-on-screen-clarifications/1103 "2021-06-02T00:03:02Z")
Hello everyone, First of all thanks for the amazing dataset, it really is full of useful information. I am working on the neuropixel data and I am trying to track the pupil movement of the mouse over the screen to comp… --- ## [Tissue Enrichment Tool](https://community.brain-map.org/t/tissue-enrichment-tool/1080)
**Author:** [@JoyOtten](https://community.brain-map.org/u/JoyOtten)\ **Replies:** 2\ **Last updated:** [May 18, 2021, 8:08am UTC](https://community.brain-map.org/t/tissue-enrichment-tool/1080 "2021-05-18T08:08:09Z")
Dear Allen Team, I was wondering if there were tissue enrichment tools available for the mouse brain atlas. Since, I’m interested in genes that are specifically expressed in one region for example the hippocampus vs the… --- ## [AHBA genotype info](https://community.brain-map.org/t/ahba-genotype-info/644)
**Author:** [@fye](https://community.brain-map.org/u/fye)\ **Replies:** 5\ **Last updated:** [April 21, 2021, 7:48pm UTC](https://community.brain-map.org/t/ahba-genotype-info/644 "2021-04-21T19:48:51Z")
Hi guys, I am working with the AHBA data, and I’m trying to find the ApoE genotype info (e.g. 3/3, 3/4) for the six donors. Is this data currently available? If so, could someone help me access the data? Thank you! --- ## [DTT in nuclei isolation](https://community.brain-map.org/t/dtt-in-nuclei-isolation/1028)
**Author:** [@Martina17](https://community.brain-map.org/u/Martina17)\ **Replies:** 1\ **Last updated:** [April 13, 2021, 9:24pm UTC](https://community.brain-map.org/t/dtt-in-nuclei-isolation/1028 "2021-04-13T21:24:54Z")
Hi, I am working with isolation of nuclei from human prefrontal cortex. The protocol I am currently using can be summarized as follows: tissue homogenization using dounce homogenizer followed by a clean-up that is carr… --- ## [Technical information regarding images (TBI project)](https://community.brain-map.org/t/technical-information-regarding-images-tbi-project/1009)
**Author:** [@Zaki](https://community.brain-map.org/u/Zaki)\ **Replies:** 2\ **Last updated:** [March 30, 2021, 7:15am UTC](https://community.brain-map.org/t/technical-information-regarding-images-tbi-project/1009 "2021-03-30T07:15:38Z")
Hi everybody! I used API to download images from Aging, Dementia and Traumatic Brain Injury Project that were stained for amyloid beta for a image analysis paper we were writing. I wrote in the materials and methods of t… --- ## [About how we are using singal processing](https://community.brain-map.org/t/about-how-we-are-using-singal-processing/996)
**Author:** [@banapuram](https://community.brain-map.org/u/banapuram)\ **Replies:** 1\ **Last updated:** [March 16, 2021, 5:23pm UTC](https://community.brain-map.org/t/about-how-we-are-using-singal-processing/996 "2021-03-16T17:23:42Z")
how we are plotting the stimulations graphs and analysis with the signal processing I want to the more topic --- ## [Gabor patch data - units](https://community.brain-map.org/t/gabor-patch-data-units/938)
**Author:** [@cspurandare](https://community.brain-map.org/u/cspurandare)\ **Replies:** 5\ **Last updated:** [March 15, 2021, 8:54pm UTC](https://community.brain-map.org/t/gabor-patch-data-units/938 "2021-03-15T20:54:00Z")
Hello, I am using the Neuropixel data, and analyzing the Gabor patch presentations. The technical white paper says that the 20 degree patches were presented in a 9 x 9 grid, and indeed the x\_pos and y\_pos for these stim… --- ## [Doubts about mouse RNA-Seq single cell data](https://community.brain-map.org/t/doubts-about-mouse-rna-seq-single-cell-data/872)
**Author:** [@ABP](https://community.brain-map.org/u/ABP)\ **Replies:** 4\ **Last updated:** [March 8, 2021, 11:26pm UTC](https://community.brain-map.org/t/doubts-about-mouse-rna-seq-single-cell-data/872 "2021-03-08T23:26:41Z")
Hi Allen Community, I’m trying to compare mouse RNA-Seq single cell data \[WHOLE CORTEX & HIPPOCAMPUS - 10X GENOMICS (2020) WITH 10X-SMART-SEQ TAXONOMY (2020)\] with my own proteomic data. My goal, among other things, is … [Next page](https://community.brain-map.org/tag/experiment-design/37.md?match_all_tags=true&page=1&tags%5B%5D=experiment-design)