Merge branch 'docs' into develop

Author: oliche

examples/data_release/2025_data_release_autism_davatolhagh.md

@@ -0,0 +1,34 @@
+# 2025 - Autism Widefield
+
+Widefield data were collected in 5 mice performing the [IBL task](https://pubmed.ncbi.nlm.nih.gov/34011433/). 
+Animals were either wildtype, or from the autism models TRE-GCaMP6s-CAMKII; NRXN KO.
+
+## Overview of the Data
+
+| Subject | Experimental Sessions |  Strain |
+|:--------|----------------------:|--------:|
+| FD_14   |                     3 | NRXN WT |
+| FD_21   |                     4 | NRXN WT |
+| FD_24   |                     4 | NRXN WT |
+| FD_28   |                     3 | NRXN KO |
+| FD_36   |                     3 | NRXN KO |
+| Total   |                    17 |       - |
+
+## Data structure and download
+The organisation of the data follows the standard IBL data structure.
+
+Please see
+
+* [These instructions](https://int-brain-lab.github.io/iblenv/notebooks_external/data_structure.html) to download an example dataset for one session, and get familiarised with the data structure
+* [These instructions](https://int-brain-lab.github.io/iblenv/notebooks_external/data_download.html) to learn how to use the ONE-api to search and download the released datasets
+* [These instructions](https://int-brain-lab.github.io/iblenv/loading_examples.html) to get familiarised with specific data loading functions
+
+Note:
+
+* The tag associated to this release is `2025_Q3_Davatolhagh_et_al_autism`
+
+
+## How to cite this dataset
+If you are using this dataset for your research please cite _Davatolhagh, M.F., Couto, J., Melin, M., Oesch, L.T., Findling, C., Morales, P., Hong, I., International Brain Laboratory, Churchland, A.K. Altered Use of Prior Expectations Shapes Behavior and Neural Dynamics in a Mouse Model of Autism_ in preparation.
+  
+

examples/data_release/2025_data_release_autism_noel.md

@@ -18,15 +18,17 @@ We recommend you download the data via ONE.
 
 ## Overview of the Data
 We have released data from 198 Neuropixel experimental sessions, with single Neuropixel recordings, referred to as probe insertions. Those were obtained with 62 genetically modified subjects performing the IBL task.
-As output of spike-sorting, there are XXX units; of which XXX are considered to be of good quality. In total, XXX brain regions were recorded in sufficient numbers for comparison with IBL’s analyses [(IBL et al. 2023)](https://doi.org/10.1101/2023.07.04.547681).
+As output of spike-sorting, there are 71,067 units; of which 12,163 are passing IBL automated quality control.
 
 
-| Model    | Subject Count | Neuropixel Count |
-|----------|---------------| --- |
-| Wildtype | 15 | 51|
-| Cntnap2  | 17 | 52|
-| Shank3b  | 15 | 41|
-| Fmr1     | 15 | 54|
+
+| Strain   | Subject Count | Recording Count | Units Count | Good Units Count |
+|:---------|--------------:|----------------:|------------:|-----------------:|
+| Cntnap2  |            17 |              52 |      20,467 |             2683 |
+| Fmr1     |            15 |              54 |      17,801 |             3491 |
+| Shank3t  |            15 |              41 |      16,357 |             2911 |
+| Wildtype |            15 |              51 |      16,442 |             3078 |
+| Total    |            62 |             198 |      71,067 |           12,163 |
 
 ## Data structure and download
 The organisation of the data follows the standard IBL data structure.
@@ -45,18 +47,17 @@ Note:
 ## How to cite this dataset
 If you are using this dataset for your research please cite:
 - the paper [A common computational and neural anomaly across mouse models of autism](https://doi.org/10.1038/s41593-025-01965-8)
-- if you download the data via ONE (recommended), cite the DOI: 10.6084/m9.figshare.30024880
+- if you download the data via ONE (recommended), cite the DOI: [10.6084/m9.figshare.30024880](https://figshare.com/account/articles/30024880?file=57596791)
 
 - if you download the data via OSF (not recommended), please use the OSF DOI.
 
 ## Data release notes and changelog
 
 ### 2025-08-29: initial release
 
-Possible future evolutions
+Possible future evolutions:
 - Spike sorting re-run with iblsorter or newer algorithm to have better yield and better pre-processing
-- Perform the missing alignments with an automatic tool to get
-
+- Perfom new alignments of the brain region labels with regards to the ephys signatures using an automatic tool
 
 #### Excluded sessions
 

examples/data_release/2025_data_release_brainwidemap.md

@@ -3,7 +3,7 @@
 IBL aims to understand the neural basis of decision-making in the mouse by gathering a whole-brain activity map composed of electrophysiological recordings pooled from multiple laboratories.
 We have systematically recorded from nearly all major brain areas with Neuropixels probes, using a grid system for unbiased sampling and replicating each recording site in at least two laboratories.
 These data have been used to construct a brain-wide map of activity at single-spike cellular resolution during a [decision-making task]((https://elifesciences.org/articles/63711)).
-Please read the associated article [(IBL et al. 2023)](https://doi.org/10.1101/2023.07.04.547681).
+Please read the associated article [(IBL et al. 2025)](https://www.nature.com/articles/s41586-025-09235-0).
 In addition to the map, this data set contains other information gathered during the task: sensory stimuli presented to the mouse; 
 mouse decisions and response times; and mouse pose information from video recordings and DeepLabCut analysis.
 Please read our accompanying [technical paper](https://doi.org/10.6084/m9.figshare.21400815) for details on the experiment and data processing pipelines.
@@ -13,7 +13,7 @@ To explore the data, visit [our vizualisation website](https://viz.international
 We have released data from 459 Neuropixel experimental sessions, which encompass 699 distinct recordings,
 referred to as probe insertions. Those were obtained with 139 subjects performing the IBL task across 12 different laboratories.
 As output of spike-sorting, there are 621,733 units; of which 75,708 are considered to be of good quality.
-In total, 241 brain regions were recorded in sufficient numbers for inclusion in IBL’s analyses [(IBL et al. 2023)](https://doi.org/10.1101/2023.07.04.547681).
+In total, 241 brain regions were recorded in sufficient numbers for inclusion in IBL’s analyses [(IBL et al. 2025)](https://doi.org/10.1101/2023.07.04.547681).
 
 
 ## Data structure and download