Merge pull request #245 from JaneliaSciComp/update-cellpose-suite2p-k…

…ilosort

Update cellpose suite2p kilosort

src/content/config.ts

@@ -7,14 +7,14 @@ const projectsCollection = defineCollection({
     title: z.string(),
     tagline: z.string(),
     maintainer: z.string(),
-    "preferred contact method": z.string(),
     "project type": z.array(z.string()),
     "OSSI proposal link": z.string().optional(),
     "github link": z.string(),
     "documentation link": z.string(),
     "installation instructions link": z.string().optional(),
     "how to cite text": z.union([z.string(), z.undefined(), z.null()]),
     "how to cite link": z.union([z.string(), z.undefined(), z.null()]),
+    "preferred contact method": z.string().optional(),
     "additional links array": z.array(z.string()).optional(),
     "additional links text array": z.array(z.string()).optional(),
     "related blog posts": z.union([

src/content/projects/_project-template.md

@@ -2,13 +2,13 @@
 title: Required. Your project title.
 tagline: "Required. 1-2 sentences that describe your project. An aside: if you use a colon in a field value, you must wrap the entire phrase in quotes. Otherwise, quotes are not required."
 maintainer: Required. Name of the person responsible for maintaining this project page. For internal use/reference - not posted to the website.
-preferred contact method: Required. Preferred way for users to reach out for help (e.g., a link to the GitHub repo's issues, Image.sc forum, or email in the format of mailto:[email protected])
 #project type - Required. Pick one of the three options - delete the other two.
 project type: [OSSI - current, OSSI - alumni, Other]
 OSSI proposal link: Required if your project is OSSI-funded. Preferred - upload the proposal as a PDF to `public/proposals` and provide the link in the format `../../proposals/PROPOSAL.pdf`. Other option - URL to the externally hosted proposal.
 github link: Required. Link to GitHub repository
 documentation link: Required. Link to documentation - can be the same as the GitHub repo if the README is the documentation
 installation instructions link: Required. Link to installation instructions - can be the same as the GitHub repo
+preferred contact method: "Creates the link for the 'Reach out for help' button on the project page. Encouraged if there is a preferred way for users to reach out for help other than creating an issue in the project's GitHub repo. Examples: link to Image.sc forum, or an email in the format of mailto:[email protected]."
 how to cite text: "If your software doesn't have an associated published paper or DOI, delete or comment-out this field to use your GitHub repo as the default. Otherwise, provide the citation for your software - wrap in quotes to ensure colons are interpreted correctly. "
 how to cite link: "https://doi.org/example - wrap entire link in quotes. If a DOI is not available, then delete or comment-out this field to use your GitHub repo as the default."
 additional links array:

src/content/projects/cellpose.md

@@ -2,16 +2,15 @@
 title: Cellpose
 tagline: A generalist algorithm for cell and nucleus segmentation (v1.0) that can be optimized for your own data (v2.0) and perform image restoration (v3.0).
 maintainer: Carsen Stringer
-preferred contact method: https://forum.image.sc/tag/cellpose
 project type: [OSSI - current]
 OSSI proposal link: ../../proposals/suite2p_and_cellpose.pdf
 github link: https://github.com/MouseLand/cellpose
 documentation link: https://cellpose.readthedocs.io/en/latest/
 installation instructions link: https://github.com/MouseLand/cellpose?tab=readme-ov-file#installation
 how to cite link: https://doi.org/10.1038/s41592-020-01018-x
 how to cite text: "Stringer, C., Wang, T., Michaelos, M., & Pachitariu, M. (2021). Cellpose: a generalist algorithm for cellular segmentation. Nature methods, 18(1), 100-106."
-# additional links array: []
-# additional links text array: []
+additional links array: [https://forum.image.sc/tag/cellpose]
+additional links text array: [Cellpose on Image.sc]
 # related blog posts: [Only-for-blog-posts-hosted-on-this-site, Optional-file-name]
 # image file: ./optional-file-path.jpg
 # image alt text: Alt text is required if you upload an image file

src/content/projects/kilosort.md

@@ -2,7 +2,6 @@
 title: Kilosort
 tagline: Maintain and develop python version of Kilosort (electrophysiology data).
 maintainer: Carsen Stringer
-preferred contact method: mailto:[email protected]
 project type: [OSSI - current]
 OSSI proposal link: ../../proposals/kilosort.pdf
 github link: https://github.com/MouseLand/Kilosort
@@ -23,9 +22,9 @@ how to cite text: Pachitariu, M., Sridhar, S., Pennington, J., & Stringer, C. (2
 related blog posts: [working-with-ossi-supported-projects]
 # image file: ./optional-file-path.jpg
 # image alt text: Alt text is required if you upload an image file
-youtube url: https://www.youtube.com/watch?v=cmrAhhquC9E
-youtube caption: 2021 Lecture - Spike sorting with Kilosort - Marius Pachitariu (HHMI)
-development team: Pachitariu Lab
+youtube url: https://www.youtube.com/watch?v=LTSmoACr918
+youtube caption: Lecture on Kilosort by Marius Pachitariu at the 2023 UCL Neuropixels Course
+development team: [Pachitariu Lab, Stringer Lab]
 programming language: ["MATLAB", "Python"]
 open source license: GPL-2.0
 software type: Package

src/content/projects/suite2p.md

@@ -2,7 +2,6 @@
 title: Suite2p
 tagline: Pipeline for processing two-photon calcium imaging data.
 maintainer: Carsen Stringer
-preferred contact method: mailto:[email protected]
 project type: [OSSI - current]
 OSSI proposal link: ../../proposals/suite2p_and_cellpose.pdf
 github link: https://github.com/MouseLand/suite2p