Staff View: :: Library Catalog

Saved in:

Bibliographic Details
Main Authors:	Coghill, Ian, Lahlou, Alienor, Lodetti, Andrea, Matsubara, Shizue, Boucle, Johann, Saux, Thomas Le, Jullien, Ludovic
Format:	Preprint
Published:	2025
Subjects:	Instrumentation and Detectors Optics
Online Access:	https://arxiv.org/abs/2506.20270
Tags:	Add Tag No Tags, Be the first to tag this record!

_version_	1866911152279126016
author	Coghill, Ian Lahlou, Alienor Lodetti, Andrea Matsubara, Shizue Boucle, Johann Saux, Thomas Le Jullien, Ludovic
author_facet	Coghill, Ian Lahlou, Alienor Lodetti, Andrea Matsubara, Shizue Boucle, Johann Saux, Thomas Le Jullien, Ludovic
contents	Luminescence imaging is invaluable for studying biological and material systems, particularly when advanced protocols that exploit temporal dynamics are employed. However, implementing such protocols often requires custom instrumentation, either modified commercial systems or fully bespoke setups, which poses a barrier for researchers without expertise in optics, electronics, or software. To address this, we present a versatile macroscopic fluorescence imaging system capable of supporting a wide range of protocols, and provide detailed build instructions along with open-source software to enable replication with minimal prior experience. We demonstrate its broad utility through applications to plants, reversibly photoswitchable fluorescent proteins, and optoelectronic devices.
format	Preprint
id	arxiv_https___arxiv_org_abs_2506_20270
institution	arXiv
publishDate	2025
record_format	arxiv
spellingShingle	Versatile luminescence macroscope with dynamic illumination for photoactive systems Coghill, Ian Lahlou, Alienor Lodetti, Andrea Matsubara, Shizue Boucle, Johann Saux, Thomas Le Jullien, Ludovic Instrumentation and Detectors Optics Luminescence imaging is invaluable for studying biological and material systems, particularly when advanced protocols that exploit temporal dynamics are employed. However, implementing such protocols often requires custom instrumentation, either modified commercial systems or fully bespoke setups, which poses a barrier for researchers without expertise in optics, electronics, or software. To address this, we present a versatile macroscopic fluorescence imaging system capable of supporting a wide range of protocols, and provide detailed build instructions along with open-source software to enable replication with minimal prior experience. We demonstrate its broad utility through applications to plants, reversibly photoswitchable fluorescent proteins, and optoelectronic devices.
title	Versatile luminescence macroscope with dynamic illumination for photoactive systems
topic	Instrumentation and Detectors Optics
url	https://arxiv.org/abs/2506.20270

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
language	"en"
ui	"standard"
VUFIND_SESSION	"9a3d5f3ebd1c32d70170147ee1488c21"

Session

Key	Value
__Laminas	array:2 [`"_REQUEST_ACCESS_TIME" => 1784525308.5364 "_VALID" => array:1 [ "Laminas\Session\Validator\Id" => "9a3d5f3ebd1c32d70170147ee1488c21" ]`]
SessionState	Laminas\Stdlib\ArrayObject {#938}
FlashMessenger	Laminas\Stdlib\ArrayObject {#1583}
SessionHelper	Laminas\Stdlib\ArrayObject {#1775}

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	"language=en; ui=standard; VUFIND_SESSION=9a3d5f3ebd1c32d70170147ee1488c21"
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	"216.73.216.85"
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	"56829"
REDIRECT_URL	""" /Record/\n arxiv_https___arxiv_org_abs_2506_20270/Details """
GATEWAY_INTERFACE	"CGI/1.1"
SERVER_PROTOCOL	"HTTP/1.1"
REQUEST_METHOD	"GET"
QUERY_STRING	""
REQUEST_URI	"/Record/%0Aarxiv_https___arxiv_org_abs_2506_20270/Details"
SCRIPT_NAME	"/index.php"
PHP_SELF	"/index.php"
REQUEST_TIME_FLOAT	1784525308.5322
REQUEST_TIME	1784525308

Environment Variables empty

Registered Handlers

0. Whoops\Handler\PrettyPageHandler

Environment & details:

GET Data empty

POST Data empty

Files empty

Key	Value
language	"en"
ui	"standard"
VUFIND_SESSION	"9a3d5f3ebd1c32d70170147ee1488c21"

Session

Key	Value
__Laminas	array:2 [`"_REQUEST_ACCESS_TIME" => 1784525308.5364 "_VALID" => array:1 [ "Laminas\Session\Validator\Id" => "9a3d5f3ebd1c32d70170147ee1488c21" ]`]
SessionState	Laminas\Stdlib\ArrayObject {#938}
FlashMessenger	Laminas\Stdlib\ArrayObject {#1583}
SessionHelper	Laminas\Stdlib\ArrayObject {#1775}

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	"language=en; ui=standard; VUFIND_SESSION=9a3d5f3ebd1c32d70170147ee1488c21"
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	"216.73.216.85"
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	"56829"
REDIRECT_URL	""" /Record/\n arxiv_https___arxiv_org_abs_2506_20270/Details """
GATEWAY_INTERFACE	"CGI/1.1"
SERVER_PROTOCOL	"HTTP/1.1"
REQUEST_METHOD	"GET"
QUERY_STRING	""
REQUEST_URI	"/Record/%0Aarxiv_https___arxiv_org_abs_2506_20270/Details"
SCRIPT_NAME	"/index.php"
PHP_SELF	"/index.php"
REQUEST_TIME_FLOAT	1784525308.5322
REQUEST_TIME	1784525308

Environment Variables empty

Registered Handlers

0. Whoops\Handler\PrettyPageHandler

Similar Items

Environment & details:

Environment & details: