# \#python **URL:** https://community.brain-map.org/tag/python/35.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) --- ## [Mis-registration of EM image coordinates using Cloudvolume for mm^3 (minnie) volume](https://community.brain-map.org/t/mis-registration-of-em-image-coordinates-using-cloudvolume-for-mm-3-minnie-volume/3404)
**Author:** [@shandran](https://community.brain-map.org/u/shandran)\ **Replies:** 1\ **Last updated:** [June 20, 2024, 10:49pm UTC](https://community.brain-map.org/t/mis-registration-of-em-image-coordinates-using-cloudvolume-for-mm-3-minnie-volume/3404 "2024-06-20T22:49:03Z")
I am pulling the electron micrograph image data from the minnie volume (mm^3) using modified version of the tutorial notebook ImageAndSegmentationDowload.ipynb. I have used this successfully on the Layer 2/3 volume (pin… --- ## [Downloading Human ISH brain data](https://community.brain-map.org/t/downloading-human-ish-brain-data/2085)
**Author:** [@MPanday](https://community.brain-map.org/u/MPanday)\ **Replies:** 0\ **Last updated:** [January 16, 2023, 3:09pm UTC](https://community.brain-map.org/t/downloading-human-ish-brain-data/2085 "2023-01-16T15:09:44Z")
Hello, In the human brain ISH data, I’m trying to download all the samples that contain the visual cortex (e.g., within the neurotransmitter study - all the samples that contain the visual cortex). Is there a way to fil… --- ## [Gene expression "RAW" read in python](https://community.brain-map.org/t/gene-expression-raw-read-in-python/729)
**Author:** [@Momo](https://community.brain-map.org/u/Momo)\ **Replies:** 1\ **Last updated:** [October 14, 2020, 4:51pm UTC](https://community.brain-map.org/t/gene-expression-raw-read-in-python/729 "2020-10-14T16:51:27Z")
Hi, I have been trying to read “raw” files in python using the rawpy library, but I keep getting errors and it seems not to work. Would anyone please let me know a way I could read RAW files in Python? Thanks, Momo --- ## [Histology slice alignment tool \[Python\]](https://community.brain-map.org/t/histology-slice-alignment-tool-python/360)
**Author:** [@FedeClaudi](https://community.brain-map.org/u/FedeClaudi)\ **Replies:** 1\ **Last updated:** [November 21, 2019, 10:55pm UTC](https://community.brain-map.org/t/histology-slice-alignment-tool-python/360 "2019-11-21T22:55:24Z")
Hello everyone, Does anyone know of a python package to align mouse brain histological images to the CCF? Something similar to this, but in python: https://github.com/petersaj/histology. Thank you, Federico --- ## [Mouse neurons reconstruction -\> CCF alignment](https://community.brain-map.org/t/mouse-neurons-reconstruction-ccf-alignment/323)
**Author:** [@FedeClaudi](https://community.brain-map.org/u/FedeClaudi)\ **Replies:** 2\ **Last updated:** [October 31, 2019, 10:45pm UTC](https://community.brain-map.org/t/mouse-neurons-reconstruction-ccf-alignment/323 "2019-10-31T22:45:39Z")
Hi, I’m working on BrainRender, a python package to render mouse anatomical and morphological data (largely based on the Allen datasets). I’ve added the possibility to render cell morphologies from theCellTypesCache,… --- ## [Loading data from transcrip.tome file in Python with h5py](https://community.brain-map.org/t/loading-data-from-transcrip-tome-file-in-python-with-h5py/310)
**Author:** [@scidanm](https://community.brain-map.org/u/scidanm)\ **Replies:** 2\ **Last updated:** [October 16, 2019, 2:06pm UTC](https://community.brain-map.org/t/loading-data-from-transcrip-tome-file-in-python-with-h5py/310 "2019-10-16T14:06:36Z")
Hello everyone, I am trying to do some work on the mouse trancriptomics data from the Allen Brain Institute. I have downloaded the transcrip.tome file from here. From the .readme I found out that the recommended way to … --- ## [Error in query... Connection reset by peer](https://community.brain-map.org/t/error-in-query-connection-reset-by-peer/282)
**Author:** [@FedeClaudi](https://community.brain-map.org/u/FedeClaudi)\ **Replies:** 3\ **Last updated:** [September 26, 2019, 4:59pm UTC](https://community.brain-map.org/t/error-in-query-connection-reset-by-peer/282 "2019-09-26T16:59:39Z")
Hello, I have been using the Allen API to render anatomical and projection data in python (https://github.com/BrancoLab/BrainRender), but I am now getting a query error. This happens when I try to fetch tractography da… --- ## [Aligning dorsal projection of mouse common coordinate framework with wide-field images of mouse brain](https://community.brain-map.org/t/aligning-dorsal-projection-of-mouse-common-coordinate-framework-with-wide-field-images-of-mouse-brain/140)
**Author:** [@beckman16](https://community.brain-map.org/u/beckman16)\ **Replies:** 3\ **Last updated:** [August 15, 2019, 9:39am UTC](https://community.brain-map.org/t/aligning-dorsal-projection-of-mouse-common-coordinate-framework-with-wide-field-images-of-mouse-brain/140 "2019-08-15T09:39:50Z")
Hi, I am trying to register the wide-field GCaMP images to the Allen Brain Atlas. Exactly how they did is this paper- https://www.nature.com/articles/s41593-019-0357-8 Unfortunately, I am unable to get a clue as to h… --- ## [RasterMap released as Python package](https://community.brain-map.org/t/rastermap-released-as-python-package/44)
**Author:** [@justin](https://community.brain-map.org/u/justin)\ **Replies:** 0\ **Last updated:** [September 7, 2018, 9:59pm UTC](https://community.brain-map.org/t/rastermap-released-as-python-package/44 "2018-09-07T21:59:38Z")
Carsen Stringer has released the amazing RasterMap in Python!! This amazing visualization technique clusters timeseries (spikes or calcium signals) & ranks them by similarity… an awesome way to visualize high-dimensio…