update README

README.md

@@ -1,5 +1,5 @@
 # Supplemental data for Schlegel _et al._ (2023)
-This paper ["_A consensus cell type atlas from multiple connectomes reveals principles of circuit stereotypy and variation_"](https://www.biorxiv.org/content/10.1101/2023.06.27.546055v1)
+This paper ["_Whole-brain annotation and multi-connectome cell typing quantifies circuit stereotypy in Drosophila_"](https://www.biorxiv.org/content/10.1101/2023.06.27.546055v2)
 reports the systematic annotation of the FAFB-FlyWire adult female fly brain connectome including over 3,000 consensus cell types validated across two brains and three brain hemispheres. The raw annotation data will be available here for download and have also been contributed to the https://codex.flywire.ai portal and [FAFB-FlyWire CATMAID spaces](https://fafb-flywire.catmaid.org/).
 
 ## Annotations
@@ -27,7 +27,7 @@ _Supplemental Video 2: Rendering of neurons by superclass._
 
 [![IMAGE ALT TEXT](http://img.youtube.com/vi/wX8z8zG6U6s/0.jpg)](https://www.youtube.com/watch?v=wX8z8zG6U6s "Supplemental Video")
 
-_Supplemental Video 3: FlyWire hemibrain cell type matches._
+_Supplemental Video 4: FlyWire hemibrain cell type matches._
 
 
 ## Skeletons & NBLAST scores
@@ -40,19 +40,19 @@ All software used in this paper is open-source and available through Github. Som
 
 | Name             | Description |
 | ---------------- | ----------- |
-| [navis](https://github.com/navis-org/navis)            | Analysis and visualisation of neurons. Used e.g. for NBLAST.  |
+| [navis](https://github.com/navis-org/navis)            		   | Analysis and visualisation of neurons. Used e.g. for NBLAST.  |
 | [navis-flybrains](https://github.com/navis-org/navis-flybrains)  | Used to transform data between template spaces (e.g. from hemibrain to FlyWire). |
-| [fafbseg](https://github.com/flyconnectome/fafbseg-py)          | Query and analyse FlyWire data (segmentation, meshes, skeletons, annotations). |
+| [fafbseg](https://github.com/flyconnectome/fafbseg-py)           | Query and analyse FlyWire data (segmentation, meshes, skeletons, annotations). |
 | [neuprint-python](https://github.com/connectome-neuprint/neuprint-python)  | Query neuPrint instances (e.g. for the hemibrain). Developed by FlyEM (Janelia Research Campus). |
 
 ### R
 
 | Name             | Description |
 | ---------------- | ----------- |
-| [natverse](https://natverse.org)          | Analysis suite with a focus on neuroanatomical data.  |
+| [natverse](https://natverse.org)        		   | Analysis suite with a focus on neuroanatomical data.  |
 | [fafbseg](https://natverse.org/fafbseg)          | Query and analyse FlyWire data (segmentation, meshes, skeletons, annotations). |
-| [coconatfly](https://natverse.org/coconatfly) | Analysis suite for Drosophila comparative connectomics. Enables hemibrain-flywire connectivity clustering. See also [coconat](https://github.com/natverse/coconat). |
-| [neuprintr](https://natverse.org/neuprintr) | Query neuPrint instances (e.g. for the hemibrain) |
+| [coconatfly](https://natverse.org/coconatfly)    | Analysis suite for Drosophila comparative connectomics. Enables hemibrain-flywire connectivity clustering. See also [coconat](https://github.com/natverse/coconat). |
+| [neuprintr](https://natverse.org/neuprintr)      | Query neuPrint instances (e.g. for the hemibrain) |
 
 Please open an issue in the respective repository if you have questions or run into problems.
 
@@ -62,24 +62,23 @@ Skeletons, connectivity and annotations for FlyWire neurons have been imported i
 ## How to cite?
 ```bibtex
 @article {Schlegel2023,
-	author = {Philipp Schlegel and Yijie Yin and Alexander S. Bates and Sven Dorkenwald and Katharina Eichler and Paul Brooks and Daniel S. Han and Marina Gkantia and Marcia dos Santos and Eva J. Munnelly and Griffin Badalamente and Laia Serratosa Capdevila and Varun A. Sane and Markus W. Pleijzier and Imaan F.M. Tamimi and Christopher R. Dunne and Irene Salgarella and Alexandre Javier and Siqi Fang and Eric Perlman and Tom Kazimiers and Sridhar R. Jagannathan and Arie Matsliah and Amy R. Sterling and Szi-chieh Yu and Claire E. McKellar and FlyWire Consortium and Marta Costa and H. Sebastian Seung and Mala Murthy and Volker Hartenstein and Davi D. Bock and Gregory S.X.E. Jefferis},
-	title = {A consensus cell type atlas from multiple connectomes reveals principles of circuit stereotypy and variation},
+	author = {Philipp Schlegel and Yijie Yin and Alexander Shakeel Bates and Sven Dorkenwald and Katharina Eichler and Paul Brooks and Daniel S Han and Marina Gkantia and Marcia dos Santos and Eva J Munnelly and Griffin Badalamente and Laia Serratosa Capdevila and Varun Aniruddha Sane and Markus William Pleijzier and Imaan F M Tamimi and Christopher R Dunne and Irene Salgarella and Alexandre Javier and Siqi Fang and Eric Perlman and Tom Kazimiers and Sridhar R Jagannathan and Arie Matsliah and Amy R Sterling and Szi-chieh Yu and Claire E McKellar and FlyWire Consortium and Marta Costa and H. Sebastian Seung and Mala Murthy and Volker Hartenstein and Davi D Bock and Gregory S X E Jefferis},
+	title = {Whole-brain annotation and multi-connectome cell typing quantifies circuit stereotypy in Drosophila},
 	elocation-id = {2023.06.27.546055},
 	year = {2023},
 	doi = {10.1101/2023.06.27.546055},
 	publisher = {Cold Spring Harbor Laboratory},
-	abstract = {The fruit fly Drosophila melanogaster combines surprisingly sophisticated behaviour with a highly tractable nervous system. A large part of the fly{\textquoteright}s success as a model organism in modern neuroscience stems from the concentration of collaboratively generated molecular genetic and digital resources. As presented in our FlyWire companion paper1, this now includes the first full brain connectome of an adult animal. Here we report the systematic and hierarchical annotation of this ~130,000-neuron connectome including neuronal classes, cell types and developmental units (hemilineages). This enables any researcher to navigate this huge dataset and find systems and neurons of interest, linked to the literature through the Virtual Fly Brain database2. Crucially, this resource includes 4,179 cell types of which 3,166 consensus cell types are robustly defined by comparison with a second dataset, the "hemibrain" connectome3. Comparative analysis showed that cell type counts and strong connections were largely stable, but connection weights were surprisingly variable within and across animals. Further analysis defined simple heuristics for connectome interpretation: connections stronger than 10 unitary synapses or providing \>1\% of the input to a target cell are highly conserved. Some cell types showed increased variability across connectomes: the most common cell type in the mushroom body, required for learning and memory, is almost twice as numerous in FlyWire than in the hemibrain. We find evidence for functional homeostasis through adjustments of the absolute amount of excitatory input while maintaining the excitation-inhibition ratio. Finally, and surprisingly, about one third of the cell types recorded in the hemibrain connectome could not be robustly identified in the FlyWire connectome, cautioning against defining cell types based on single connectomes. We propose that a cell type should be robust to inter-individual variation, and therefore defined as a group of cells that are more similar to cells in a different brain than to any other cell in the same brain. We show that this new definition can be consistently applied to whole connectome datasets. Our work defines a consensus cell type atlas for the fly brain and provides both an intellectual framework and open source toolchain for brain-scale comparative connectomics.Competing Interest StatementH. S. Seung declares a financial interest in Zetta AI.},
-	URL = {https://www.biorxiv.org/content/early/2023/06/27/2023.06.27.546055},
-	eprint = {https://www.biorxiv.org/content/early/2023/06/27/2023.06.27.546055.full.pdf},
+	URL = {https://www.biorxiv.org/content/early/2023/07/15/2023.06.27.546055},
+	eprint = {https://www.biorxiv.org/content/early/2023/07/15/2023.06.27.546055.full.pdf},
 	journal = {bioRxiv}
 }
-
 ```
 
 ## Changelog
 Because annotations are still evolving we might occasionally update them. You can always go back to the state at the time of the paper using the tags!
 
-- [`1.0.0`](https://github.com/flyconnectome/flywire_annotations/releases/tag/v1.0.0): First release matching the Schlegel *et al*. bioRxiv paper.
+- [`1.1.0`](https://github.com/flyconnectome/flywire_annotations/releases/tag/v1.1.0): Second release for the updated Schlegel *et al*. bioRxiv version
+- [`1.0.0`](https://github.com/flyconnectome/flywire_annotations/releases/tag/v1.0.0): First release matching the Schlegel *et al*. bioRxiv paper
 
 ## Found a broken link?
 Please open an [issue](https://github.com/flyconnectome/flywire_annotations/issues).