{"id":12130,"date":"2021-01-13T09:30:00","date_gmt":"2021-01-13T11:30:00","guid":{"rendered":"https:\/\/mindthegraph.com\/blog\/?p=12130"},"modified":"2022-10-18T08:09:26","modified_gmt":"2022-10-18T11:09:26","slug":"pyscratch-spatial-and-temporal-information-from-scratch-assays","status":"publish","type":"post","link":"https:\/\/mindthegraph.com\/blog\/sk\/pyscratch-spatial-and-temporal-information-from-scratch-assays\/","title":{"rendered":"PyScratch: Nov\u00fd n\u00e1stroj na spracovanie priestorov\u00fdch a \u010dasov\u00fdch inform\u00e1ci\u00ed zo scratchov\u00fdch anal\u00fdz"},"content":{"rendered":"

PyScratch je nov\u00fd softv\u00e9r s otvoren\u00fdm zdrojov\u00fdm k\u00f3dom implementovan\u00fd v jazyku Python na anal\u00fdzu migra\u010dn\u00fdch d\u00e1tov\u00fdch anal\u00fdz, ktor\u00fd m\u00e1 u\u017e\u00edvate\u013esky pr\u00edvetiv\u00e9 rozhranie umo\u017e\u0148uj\u00face jeho pou\u017e\u00edvanie vedcom s mal\u00fdmi alebo \u017eiadnymi program\u00e1torsk\u00fdmi zru\u010dnos\u0165ami. <\/p>\n\n\n\n

Softv\u00e9r bol navrhnut\u00fd v spolupr\u00e1ci troch braz\u00edlskych vedcov v laborat\u00f3riu NanoCell Interactions na univerzite v Campinas v roku 2017. <\/p>\n\n\n\n

Vznikol z potreby t\u00fdchto vedcov a dnes je cie\u013eom softv\u00e9ru u\u013eah\u010di\u0165 ka\u017edodenn\u00fa prax v\u00fdskumn\u00edkov, vyl\u00fa\u010di\u0165 manu\u00e1lnu anal\u00fdzu, zv\u00fd\u0161i\u0165 reprodukovate\u013enos\u0165 a minimalizova\u0165 \u013eudsk\u00e9 chyby.<\/p>\n\n\n\n

\"\"<\/a><\/figure><\/div>\n\n\n\n

Anal\u00fdza obrazu je jedn\u00fdm z najd\u00f4le\u017eitej\u0161\u00edch sp\u00f4sobov, ktor\u00e9 vedci pou\u017e\u00edvaj\u00fa v r\u00f4znych metodik\u00e1ch na anal\u00fdzu v\u00fdsledkov. <\/p>\n\n\n\n

V posledn\u00fdch rokoch sa zv\u00fd\u0161ilo nielen pou\u017e\u00edvanie automatick\u00fdch mikroskopov, ale aj zlo\u017eitos\u0165 z\u00edskan\u00fdch \u00fadajov. <\/p>\n\n\n\n

S\u00fa\u010das\u0165ou pr\u00e1ce vedca je objavova\u0165, ako zaobch\u00e1dza\u0165 s nov\u00fdm druhom inform\u00e1ci\u00ed, okrem toho analyzova\u0165 a spracov\u00e1va\u0165 \u00fadaje. <\/p>\n\n\n\n

Na to vedci potrebuj\u00fa kvalitn\u00e9 a \u0161pecializovan\u00e9 n\u00e1stroje na spr\u00e1vne z\u00edskavanie a interpret\u00e1ciu v\u0161etk\u00fdch \u00fadajov.<\/p>\n\n\n\n

PyScratch bol prv\u00fdkr\u00e1t vytvoren\u00fd, aby pomohol Fernande Garcia-Fossa, v\u00fdskumnej biologi\u010dke, analyzova\u0165 obrovsk\u00e9 mno\u017estvo \u00fadajov z jej migra\u010dn\u00fdch testov. <\/p>\n\n\n\n

\"Vykonal som po\u0161kriabanie rakovinov\u00fdch buniek a inkuboval som ich v zariaden\u00ed 48 hod\u00edn, pri\u010dom som ka\u017ed\u00fdch 15 min\u00fat z\u00edskaval obr\u00e1zky a na konci len jedn\u00e9ho experimentu som mal asi tis\u00edc obr\u00e1zkov, ktor\u00e9 som si mohol pozrie\u0165 a analyzova\u0165! <\/p>\n\n\n\n

Ru\u010dne to nebolo mo\u017en\u00e9,\" hovor\u00ed Garcia-Fossa. Pri rie\u0161en\u00ed tohto probl\u00e9mu sa Garcia-Fossa obr\u00e1tila na svojho partnera, fyzika Vladim\u00edra Gaala, aby jej pomohol, pri\u010dom Gaal sa v tom \u010dase u\u010dil Python, \u010do bola skvel\u00e1 pr\u00edle\u017eitos\u0165, ako tieto znalosti uplatni\u0165 v praxi.<\/p>\n\n\n\n

Obaja teda pracovali v rie\u0161en\u00ed prostredn\u00edctvom rutiny Python, ktor\u00e1 rozpoznala po\u0161kriaban\u00e9 oblasti a exportovala ich do s\u00faboru csv. <\/p>\n\n\n\n

\"S prib\u00fadaj\u00facim \u010dasom sme poc\u00edtili potrebu vyvin\u00fa\u0165 pou\u017e\u00edvate\u013esk\u00e9 rozhranie, ktor\u00e9 by e\u0161te viac u\u013eah\u010dilo pou\u017e\u00edvanie, a tak by sme mohli softv\u00e9r zverejni\u0165 aj pre v\u0161etk\u00fdch v\u00fdskumn\u00edkov, ktor\u00ed by ho potrebovali pou\u017e\u00edva\u0165\", hovor\u00ed Garcia-Fossa o \u010dl\u00e1nku o softv\u00e9ri, ktor\u00fd si m\u00f4\u017eete pozrie\u0165 kliknut\u00edm sem<\/a>.<\/p>\n\n\n\n

Garcia-Fossa tie\u017e hovor\u00ed, \u017ee im chv\u00ed\u013eu trvalo, k\u00fdm zo sn\u00edmok rozpoznali a definovali migra\u010dn\u00fa oblas\u0165, preto\u017ee sn\u00edmky sa m\u00f4\u017eu navz\u00e1jom ve\u013emi l\u00ed\u0161i\u0165 kv\u00f4li svetlu, zaostreniu a kontrastu, a dnes pou\u017e\u00edvan\u00e1 verzia u\u017e dok\u00e1\u017ee analyzova\u0165 celkom dobre. <\/p>\n\n\n\n

Napriek tomu na softv\u00e9ri st\u00e1le pracuj\u00fa a uv\u00e1dzaj\u00fa nov\u00e9 a lep\u0161ie verzie, preto\u017ee zverejnen\u00fd \u010dl\u00e1nok priniesol niektor\u00e9 potreby na zlep\u0161enie na z\u00e1klade po\u017eiadaviek pou\u017e\u00edvate\u013eov.<\/p>\n\n\n\n

Test pou\u017e\u00edvan\u00fd na overenie v\u00fdkonnosti softv\u00e9ru, migra\u010dn\u00fd test, test po\u0161kriabania alebo hojenia r\u00e1n, je testom be\u017ene pou\u017e\u00edvan\u00fdm v biol\u00f3gii, preto\u017ee umo\u017e\u0148uje analyzova\u0165 z\u00e1kladn\u00fd mechanizmus fyziologick\u00fdch a patologick\u00fdch bunkov\u00fdch udalost\u00ed. <\/p>\n\n\n\n

\u0160t\u00fadium hojenia r\u00e1n je okrem angiogen\u00e9zy a v\u00fdvoja n\u00e1dorov d\u00f4le\u017eit\u00fdm sp\u00f4sobom na pochopenie v\u00fdvoja a modelovania tkan\u00edv. <\/p>\n\n\n\n

Ak sa test vykon\u00e1va v dvoch rozmeroch, je mo\u017en\u00e9 mera\u0165, ako r\u00fdchlo bunky reaguj\u00fa na ranu, ktor\u00e1 pokr\u00fdva definovan\u00fa oblas\u0165.<\/p>\n\n\n\n

In\u00fdmi slovami, experiment v podstate spo\u010d\u00edva vo vytvoren\u00ed medzery v monovrstve konfluen\u010dn\u00fdch buniek v plaku. <\/p>\n\n\n\n

V priebehu \u010dasu za\u010dn\u00fa bunky migrova\u0165, aby vyplnili medzeru, a r\u00fdchlos\u0165 migr\u00e1cie buniek sa m\u00f4\u017ee mera\u0165. <\/p>\n\n\n\n

Na meranie migra\u010dnej r\u00fdchlosti buniek potom potrebuj\u00fa z\u00edska\u0165 sn\u00edmky, ich mno\u017estvo, \u010do je zase problematick\u00fd krok anal\u00fdzy, preto\u017ee si vy\u017eaduje manu\u00e1lne meranie. <\/p>\n\n\n\n

Na\u0161\u0165astie dnes m\u00e1me k dispoz\u00edcii mno\u017estvo technol\u00f3gi\u00ed na zlep\u0161enie a moderniz\u00e1ciu na\u0161ej anal\u00fdzy, ktor\u00e9 vedcom umo\u017e\u0148uj\u00fa prija\u0165 lep\u0161ie a personalizovanej\u0161ie sp\u00f4soby z\u00edskavania v\u00fdsledkov. <\/p>\n\n\n\n

Tak ako to urobili Garcia-Fossa a Gaal.<\/p>\n\n\n\n

V s\u00fa\u010dasnosti je mo\u017en\u00e9 n\u00e1js\u0165 \u010fal\u0161ie komer\u010dn\u00e9 a nekomer\u010dn\u00e9 n\u00e1stroje na spracovanie oblasti r\u00e1n. <\/p>\n\n\n\n

Nie s\u00fa v\u0161ak tak\u00e9 jednoduch\u00e9 ako PyScratch a vy\u017eaduj\u00fa od pou\u017e\u00edvate\u013ea ur\u010dit\u00fa \u00farove\u0148 programovania a tie\u017e vy\u017eaduj\u00fa od pou\u017e\u00edvate\u013ea pozornos\u0165 na pln\u00fd \u00fav\u00e4zok, \u010d\u00edm sa anal\u00fdza st\u00e1va n\u00e1chylnej\u0161ou na \u013eudsk\u00e9 chyby, plus \u010das, ktor\u00fd v\u00fdskumn\u00edk potrebuje na anal\u00fdzu v\u0161etk\u00fdch obr\u00e1zkov a \u00fadajov.<\/p>\n\n\n\n

V \u010dl\u00e1nku autori vysvet\u013euj\u00fa, ako tento softv\u00e9r funguje. Zo v\u0161etk\u00fdch obr\u00e1zkov zhotoven\u00fdch v r\u00e1mci experimentu pou\u017e\u00edvate\u013e z\u00edska s\u00fabor s hodnotami oddelen\u00fdmi \u010diarkami (.cvs), v\u00fdstup, ktor\u00fd uchov\u00e1va tabu\u013ekov\u00e9 \u00fadaje v oby\u010dajnom texte. <\/p>\n\n\n\n

Pou\u017e\u00edvate\u013e potom m\u00f4\u017ee \u00fadaje spracova\u0165 v r\u00e1mci svojich be\u017en\u00fdch postupov. Garcia-Fossa hovor\u00ed, \u017ee program bol nevyhnutn\u00fd pre jej magistersk\u00fa pr\u00e1cu: \"Softv\u00e9r transformuje vstupn\u00e9 \u00fadaje na hodnoty, ktor\u00e9 maj\u00fa biologick\u00fd zmysel, ako napr\u00edklad r\u00fdchlos\u0165 migr\u00e1cie buniek. <\/p>\n\n\n\n

V\u010faka PyScratch som mohol lep\u0161ie analyzova\u0165 \u00fa\u010dinok mojej nano\u010dastice na bunky rakoviny prostaty a mera\u0165 r\u00fdchlos\u0165 migr\u00e1cie buniek a presn\u00fd \u010das dobr\u00e9ho uzavretia.\"<\/p>\n\n\n\n

\"\"<\/a><\/figure><\/div>\n\n\n\n

Ak chcete vysk\u00fa\u0161a\u0165 PyScratch pre svoj v\u00fdskum, softv\u00e9r je vo\u013ene dostupn\u00fd a ka\u017ed\u00fd z vedeckej komunity ho m\u00f4\u017ee pou\u017e\u00edva\u0165, \u010do pom\u00e1ha Garciovi-Fossovi a Gaalovi program vylep\u0161ova\u0165 a zdokona\u013eova\u0165.<\/p>\n\n\n\n

 ____<\/p>\n\n\n\n

Ak\u00e9 s\u00fa va\u0161e doteraj\u0161ie sk\u00fasenosti s Mind the Graph? Pom\u00f4\u017ete n\u00e1m zlep\u0161i\u0165 na\u0161u platformu pre v\u00e1s a pre mnoh\u00fdch \u010fal\u0161\u00edch vedcov uverejnen\u00edm recenzie Mind the Graph. Povedzte n\u00e1m o svojich sk\u00fasenostiach, sta\u010d\u00ed klikn\u00fa\u0165 na tu<\/a>. <\/p>","protected":false},"excerpt":{"rendered":"

PyScratch je nov\u00fd softv\u00e9r s otvoren\u00fdm zdrojov\u00fdm k\u00f3dom implementovan\u00fd v jazyku Python na anal\u00fdzu migra\u010dn\u00fdch d\u00e1tov\u00fdch anal\u00fdz, ktor\u00fd m\u00e1 u\u017e\u00edvate\u013esky pr\u00edvetiv\u00e9 rozhranie umo\u017e\u0148uj\u00face jeho pou\u017e\u00edvanie vedcom s mal\u00fdmi alebo \u017eiadnymi program\u00e1torsk\u00fdmi zru\u010dnos\u0165ami. Softv\u00e9r bol navrhnut\u00fd v spolupr\u00e1ci troch braz\u00edlskych vedcov v laborat\u00f3riu NanoCell Interactions na univerzite v Campinas v roku 2017. Bol [...]<\/p>","protected":false},"author":4,"featured_media":12133,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[959,28],"tags":[817,554,964],"yoast_head":"\nA new tool for processing spatial and temporal information<\/title>\n<meta name=\"description\" content=\"Read this blog to know what PyScratch is and how that new tool processes spatial and temporal information from scratch assays.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/mindthegraph.com\/blog\/sk\/saggi-pyscratch-spatial-and-temporal-information-from-scratch\/\" \/>\n<meta property=\"og:locale\" content=\"sk_SK\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"A new tool for processing spatial and temporal information\" \/>\n<meta property=\"og:description\" content=\"Read this blog 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He has a Ph.D. and solid scientific background in Psychopharmacology and experience as a Guest Researcher at the Max Planck Institute of Psychiatry (Germany) and Researcher in D'Or Institute for Research and Education (IDOR, Brazil). Fabricio holds over 2500 citations in Google Scholar. He has 10 years of experience in small innovative businesses, with relevant experience in product design and innovation management. Connect with him on LinkedIn - Fabricio Pamplona.","sameAs":["http:\/\/mindthegraph.com","https:\/\/www.linkedin.com\/in\/fabriciopamplona"],"url":"https:\/\/mindthegraph.com\/blog\/sk\/author\/fabricio\/"}]}},"_links":{"self":[{"href":"https:\/\/mindthegraph.com\/blog\/sk\/wp-json\/wp\/v2\/posts\/12130"}],"collection":[{"href":"https:\/\/mindthegraph.com\/blog\/sk\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/mindthegraph.com\/blog\/sk\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/mindthegraph.com\/blog\/sk\/wp-json\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/mindthegraph.com\/blog\/sk\/wp-json\/wp\/v2\/comments?post=12130"}],"version-history":[{"count":1,"href":"https:\/\/mindthegraph.com\/blog\/sk\/wp-json\/wp\/v2\/posts\/12130\/revisions"}],"predecessor-version":[{"id":12134,"href":"https:\/\/mindthegraph.com\/blog\/sk\/wp-json\/wp\/v2\/posts\/12130\/revisions\/12134"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/mindthegraph.com\/blog\/sk\/wp-json\/wp\/v2\/media\/12133"}],"wp:attachment":[{"href":"https:\/\/mindthegraph.com\/blog\/sk\/wp-json\/wp\/v2\/media?parent=12130"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/mindthegraph.com\/blog\/sk\/wp-json\/wp\/v2\/categories?post=12130"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/mindthegraph.com\/blog\/sk\/wp-json\/wp\/v2\/tags?post=12130"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}