kresnajenie/sc-schier-merfisheyes: MERFISHEYES Zebrafish v1.0.0 - Single-Cell Visualizer

Fuente: Zenodo

Enregistré dans:

Détails bibliographiques
Auteurs principaux:	Jenie, Ignatius Kresnathan Sjahnir, Lin, Edward, Chuang, Serena
Format:	Recurso digital
Publié:	Zenodo 2025
Accès en ligne:	Acceder al recurso
Tags:	Ajouter un tag Pas de tags, Soyez le premier à ajouter un tag!

_version_	1866902097199366144
author	Jenie, Ignatius Kresnathan Sjahnir Lin, Edward Chuang, Serena
author_facet	Jenie, Ignatius Kresnathan Sjahnir Lin, Edward Chuang, Serena
contents	<h1>MERFISHEYES Single-Cell Visualizer</h1> <p>Interactive web-based tool for exploring zebrafish embryonic development with integrated scRNA-seq, scATAC-seq, and MERFISH spatial transcriptomics data.</p> <h2>Features</h2> <ul> <li><strong>3D Spatial Visualization</strong>: Interactive Three.js-based visualization of cells in spatial coordinates</li> <li><strong>Multi-Modal Data</strong>: Toggle between RNA expression and chromatin accessibility views</li> <li><strong>Latent Space Exploration</strong>: View cells in UMAP embeddings</li> <li><strong>Interactive Filtering</strong>: Filter by cell type, genes, and ATAC-seq peaks</li> <li><strong>Developmental Trajectories</strong>: Explore zebrafish development from gastrulation to organogenesis</li> <li><strong>Responsive UI</strong>: Bootstrap-based interface with dynamic color scales and controls</li> </ul> <h2>Data Source</h2> <p>Data from <strong>Wan et al.</strong> (2024) - Whole-embryo Spatial Transcriptomics at Subcellular Resolution from Gastrulation to Organogenesis</p> <ul> <li>DOI: <a href="https://doi.org/10.1101/2024.08.27.609868">10.1101/2024.08.27.609868</a></li> </ul> <h2>Tech Stack</h2> <ul> <li>Vite 5.x</li> <li>Three.js for 3D rendering</li> <li>Bootstrap 5 for UI</li> <li>RxJS for reactive state management</li> <li>jQuery for DOM manipulation</li> </ul>
format	Recurso digital
id	zenodo_https___doi_org_10_5281_zenodo_17573742
institution	Zenodo
language
publishDate	2025
publisher	Zenodo
record_format	zenodo
spellingShingle	kresnajenie/sc-schier-merfisheyes: MERFISHEYES Zebrafish v1.0.0 - Single-Cell Visualizer Jenie, Ignatius Kresnathan Sjahnir Lin, Edward Chuang, Serena <h1>MERFISHEYES Single-Cell Visualizer</h1> <p>Interactive web-based tool for exploring zebrafish embryonic development with integrated scRNA-seq, scATAC-seq, and MERFISH spatial transcriptomics data.</p> <h2>Features</h2> <ul> <li><strong>3D Spatial Visualization</strong>: Interactive Three.js-based visualization of cells in spatial coordinates</li> <li><strong>Multi-Modal Data</strong>: Toggle between RNA expression and chromatin accessibility views</li> <li><strong>Latent Space Exploration</strong>: View cells in UMAP embeddings</li> <li><strong>Interactive Filtering</strong>: Filter by cell type, genes, and ATAC-seq peaks</li> <li><strong>Developmental Trajectories</strong>: Explore zebrafish development from gastrulation to organogenesis</li> <li><strong>Responsive UI</strong>: Bootstrap-based interface with dynamic color scales and controls</li> </ul> <h2>Data Source</h2> <p>Data from <strong>Wan et al.</strong> (2024) - Whole-embryo Spatial Transcriptomics at Subcellular Resolution from Gastrulation to Organogenesis</p> <ul> <li>DOI: <a href="https://doi.org/10.1101/2024.08.27.609868">10.1101/2024.08.27.609868</a></li> </ul> <h2>Tech Stack</h2> <ul> <li>Vite 5.x</li> <li>Three.js for 3D rendering</li> <li>Bootstrap 5 for UI</li> <li>RxJS for reactive state management</li> <li>jQuery for DOM manipulation</li> </ul>
title	kresnajenie/sc-schier-merfisheyes: MERFISHEYES Zebrafish v1.0.0 - Single-Cell Visualizer
url	https://doi.org/10.5281/zenodo.17573742

if (filemtime($filename) + $maxlifetime < time()) { unlink($filename); $count++; } } return $count; } /** * A function that is called internally when session data is to be saved. * * @param string $sessId The current session ID * @param string $data The session data to write * * @return bool */ protected function saveSession($sessId, $data): bool { $sessFile = $this->path . '/sess_' . $sessId; if ($handle = fopen($sessFile, 'w')) { $return = false; // Lock the file for exclusive access to avoid issues with multiple // processes writing session simultaneously: if (flock($handle, LOCK_EX)) { $return = fwrite($handle, $data); // Make sure that there's no trailing data by truncating the file to // the correct length: ftruncate($handle, strlen($data)); fflush($handle); flock($handle, LOCK_UN); } fclose($handle); if ($return !== false) { return true; } } // If we got this far, something went wrong with the file output... // It is tempting to throw an exception here, but this code is called // outside of the context of exception handling, so all we can do is // echo a message.

// Anecdotal testing Today and Yesterday seems to indicate destroy() // is called by the garbage collector and everything is good. // Something to keep in mind though. return 0; } /** * Write function that is called when session data is to be saved. * * @param string $sessId The current session ID * @param string $data The session data to write * * @return bool */ public function write($sessId, $data): bool { if ($this->writesDisabled) { return true; } return $this->saveSession($sessId, $data); } /** * A function that is called internally when session data is to be saved. * * @param string $sessId The current session ID * @param string $data The session data to write * * @return bool */ abstract protected function saveSession($sessId, $data): bool; }

* * @return void */ public function writeClose() { // The assumption is that we're using PHP's ext/session. // session_write_close() will actually overwrite $_SESSION with an // empty array on completion -- which leads to a mismatch between what // is in the storage object and $_SESSION. To get around this, we // temporarily reset $_SESSION to an array, and then re-link it to // the storage object. // // Additionally, while you _can_ write to $_SESSION following a // session_write_close() operation, no changes made to it will be // flushed to the session handler. As such, we now mark the storage // object isImmutable. $storage = $this->getStorage(); if (! $storage->isImmutable()) { $_SESSION = $storage->toArray(true); session_write_close(); $storage->fromArray($_SESSION); $storage->markImmutable(); } } /** * Attempt to set the session name * * If the session has already been started, or if the name provided fails * validation, an exception will be raised. * * @param string $name * @return SessionManager * @throws Exception\InvalidArgumentException */ public function setName($name) { if ($this->sessionExists()) { throw new Exception\InvalidArgumentException( 'Cannot set session name after a session has already started'

Environment & details:

GET Data empty

POST Data empty

Files empty

Key	Value
ui	"standard"
VUFIND_SESSION	"914e4c2a006e7518e56078f8239b1725"
language	"fr"

Session

Key	Value
__Laminas	array:2 [`"_REQUEST_ACCESS_TIME" => 1790782790.1331 "_VALID" => array:1 [ "Laminas\Session\Validator\Id" => "914e4c2a006e7518e56078f8239b1725" ]`]
SessionState	Laminas\Stdlib\ArrayObject {#938}
FlashMessenger	Laminas\Stdlib\ArrayObject {#1428}
SessionHelper	Laminas\Stdlib\ArrayObject {#1760}

Server/Request Data

Key	Value
REDIRECT_VUFIND_LOCAL_DIR	"/usr/local/vufind/local"
REDIRECT_HTTPS	"on"
REDIRECT_SSL_TLS_SNI	"info.umar.mx"
REDIRECT_STATUS	"200"
VUFIND_LOCAL_DIR	"/usr/local/vufind/local"
HTTPS	"on"
SSL_TLS_SNI	"info.umar.mx"
HTTP_ACCEPT	"/"
HTTP_USER_AGENT	"Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)"
HTTP_COOKIE	"ui=standard; VUFIND_SESSION=914e4c2a006e7518e56078f8239b1725; language=fr"
HTTP_ACCEPT_ENCODING	"gzip, br, zstd, deflate"
HTTP_HOST	"info.umar.mx"
PATH	"/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/snap/bin"
SERVER_SIGNATURE	"<address>Apache/2.4.66 (Ubuntu) Server at info.umar.mx Port 443</address>\n"
SERVER_SOFTWARE	"Apache/2.4.66 (Ubuntu)"
SERVER_NAME	"info.umar.mx"
SERVER_ADDR	"200.23.222.19"
SERVER_PORT	"443"
REMOTE_ADDR	"216.73.216.147"
DOCUMENT_ROOT	"/usr/local/vufind/public"
REQUEST_SCHEME	"https"
CONTEXT_PREFIX	""
CONTEXT_DOCUMENT_ROOT	"/usr/local/vufind/public"
SERVER_ADMIN	"admin@localhost"
SCRIPT_FILENAME	"/usr/local/vufind/public/index.php"
REMOTE_PORT	"39731"
REDIRECT_URL	"/Record/zenodo_https___doi_org_10_5281_zenodo_17573742/Details"
GATEWAY_INTERFACE	"CGI/1.1"
SERVER_PROTOCOL	"HTTP/1.1"
REQUEST_METHOD	"GET"
QUERY_STRING	""
REQUEST_URI	"/Record/zenodo_https___doi_org_10_5281_zenodo_17573742/Details"
SCRIPT_NAME	"/index.php"
PHP_SELF	"/index.php"
REQUEST_TIME_FLOAT	1790782790.1246
REQUEST_TIME	1790782790

Environment Variables empty

Registered Handlers

0. Whoops\Handler\PrettyPageHandler

Environment & details:

GET Data empty

POST Data empty

Files empty

Key	Value
ui	"standard"
VUFIND_SESSION	"914e4c2a006e7518e56078f8239b1725"
language	"fr"

Session

Key	Value
__Laminas	array:2 [`"_REQUEST_ACCESS_TIME" => 1790782790.1331 "_VALID" => array:1 [ "Laminas\Session\Validator\Id" => "914e4c2a006e7518e56078f8239b1725" ]`]
SessionState	Laminas\Stdlib\ArrayObject {#938}
FlashMessenger	Laminas\Stdlib\ArrayObject {#1428}
SessionHelper	Laminas\Stdlib\ArrayObject {#1760}

Server/Request Data

Key	Value
REDIRECT_VUFIND_LOCAL_DIR	"/usr/local/vufind/local"
REDIRECT_HTTPS	"on"
REDIRECT_SSL_TLS_SNI	"info.umar.mx"
REDIRECT_STATUS	"200"
VUFIND_LOCAL_DIR	"/usr/local/vufind/local"
HTTPS	"on"
SSL_TLS_SNI	"info.umar.mx"
HTTP_ACCEPT	"/"
HTTP_USER_AGENT	"Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)"
HTTP_COOKIE	"ui=standard; VUFIND_SESSION=914e4c2a006e7518e56078f8239b1725; language=fr"
HTTP_ACCEPT_ENCODING	"gzip, br, zstd, deflate"
HTTP_HOST	"info.umar.mx"
PATH	"/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/snap/bin"
SERVER_SIGNATURE	"<address>Apache/2.4.66 (Ubuntu) Server at info.umar.mx Port 443</address>\n"
SERVER_SOFTWARE	"Apache/2.4.66 (Ubuntu)"
SERVER_NAME	"info.umar.mx"
SERVER_ADDR	"200.23.222.19"
SERVER_PORT	"443"
REMOTE_ADDR	"216.73.216.147"
DOCUMENT_ROOT	"/usr/local/vufind/public"
REQUEST_SCHEME	"https"
CONTEXT_PREFIX	""
CONTEXT_DOCUMENT_ROOT	"/usr/local/vufind/public"
SERVER_ADMIN	"admin@localhost"
SCRIPT_FILENAME	"/usr/local/vufind/public/index.php"
REMOTE_PORT	"39731"
REDIRECT_URL	"/Record/zenodo_https___doi_org_10_5281_zenodo_17573742/Details"
GATEWAY_INTERFACE	"CGI/1.1"
SERVER_PROTOCOL	"HTTP/1.1"
REQUEST_METHOD	"GET"
QUERY_STRING	""
REQUEST_URI	"/Record/zenodo_https___doi_org_10_5281_zenodo_17573742/Details"
SCRIPT_NAME	"/index.php"
PHP_SELF	"/index.php"
REQUEST_TIME_FLOAT	1790782790.1246
REQUEST_TIME	1790782790

Environment Variables empty

Registered Handlers

0. Whoops\Handler\PrettyPageHandler

Documents similaires

Environment & details:

Environment & details: