{"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\/cs\/pyscratch-spatial-and-temporal-information-from-scratch-assays\/","title":{"rendered":"PyScratch: Nov\u00fd n\u00e1stroj pro zpracov\u00e1n\u00ed prostorov\u00fdch a \u010dasov\u00fdch informac\u00ed ze scratchov\u00fdch anal\u00fdz"},"content":{"rendered":"

PyScratch je nov\u00fd open-source software implementovan\u00fd v jazyce Python pro anal\u00fdzu migra\u010dn\u00edch dat s u\u017eivatelsky p\u0159\u00edv\u011btiv\u00fdm rozhran\u00edm, kter\u00e9 umo\u017e\u0148uje v\u011bdc\u016fm s minim\u00e1ln\u00edmi nebo \u017e\u00e1dn\u00fdmi program\u00e1torsk\u00fdmi dovednostmi jej pou\u017e\u00edvat. <\/p>\n\n\n\n

Software byl navr\u017een ve spolupr\u00e1ci t\u0159\u00ed brazilsk\u00fdch v\u011bdc\u016f v laborato\u0159i NanoCell Interactions na univerzit\u011b v Campinas v roce 2017. <\/p>\n\n\n\n

Zrodil se z pot\u0159eby t\u011bchto v\u011bdc\u016f a dnes je \u00fa\u010delem softwaru usnadnit ka\u017edodenn\u00ed praxi v\u00fdzkumn\u00fdch pracovn\u00edk\u016f, vylou\u010dit manu\u00e1ln\u00ed anal\u00fdzu, zv\u00fd\u0161it reprodukovatelnost a minimalizovat lidsk\u00e9 chyby.<\/p>\n\n\n\n

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

Anal\u00fdza obrazu je jedn\u00edm z nejd\u016fle\u017eit\u011bj\u0161\u00edch zp\u016fsob\u016f, kter\u00e9 v\u011bdci pou\u017e\u00edvaj\u00ed v r\u016fzn\u00fdch metodik\u00e1ch pro anal\u00fdzu v\u00fdsledk\u016f. <\/p>\n\n\n\n

V posledn\u00edch letech se roz\u0161\u00ed\u0159ilo nejen pou\u017e\u00edv\u00e1n\u00ed automatick\u00fdch mikroskop\u016f, ale tak\u00e9 slo\u017eitost z\u00edskan\u00fdch dat. <\/p>\n\n\n\n

Sou\u010d\u00e1st\u00ed pr\u00e1ce v\u011bdce je objevovat, jak zach\u00e1zet s nov\u00fdm druhem informac\u00ed, krom\u011b toho analyzovat a zpracov\u00e1vat data. <\/p>\n\n\n\n

K tomu v\u011bdci pot\u0159ebuj\u00ed kvalitn\u00ed a specializovan\u00e9 n\u00e1stroje, aby mohli spr\u00e1vn\u011b z\u00edskat a interpretovat v\u0161echna data.<\/p>\n\n\n\n

PyScratch byl poprv\u00e9 vytvo\u0159en, aby pomohl Fernand\u011b Garcia-Fossa, v\u00fdzkumn\u00e9 pracovnici v oblasti biologie, analyzovat obrovsk\u00e9 mno\u017estv\u00ed dat z jej\u00edch migra\u010dn\u00edch test\u016f. <\/p>\n\n\n\n

\"Provedl jsem po\u0161kr\u00e1b\u00e1n\u00ed rakovinn\u00fdch bun\u011bk a inkuboval je v za\u0159\u00edzen\u00ed po dobu 48 hodin, p\u0159i\u010dem\u017e jsem ka\u017ed\u00fdch 15 minut po\u0159izoval sn\u00edmky a na konci pouze jednoho experimentu jsem m\u011bl k dispozici asi tis\u00edc sn\u00edmk\u016f k prohl\u00ed\u017een\u00ed a anal\u00fdze! <\/p>\n\n\n\n

Ru\u010dn\u011b to ne\u0161lo,\" \u0159\u00edk\u00e1 Garcia-Fossa. S \u0159e\u0161en\u00edm tohoto probl\u00e9mu se Garcia-Fossa obr\u00e1tila na sv\u00e9ho partnera, fyzika Vladim\u00edra Gaala, kter\u00fd se v t\u00e9 dob\u011b u\u010dil Python, co\u017e byla skv\u011bl\u00e1 p\u0159\u00edle\u017eitost, jak tyto znalosti uplatnit v praxi.<\/p>\n\n\n\n

Oba tedy pracovali v \u0159e\u0161en\u00ed prost\u0159ednictv\u00edm rutiny Pythonu, kter\u00e1 rozpoznala po\u0161kr\u00e1ban\u00e9 oblasti a exportovala je do souboru csv. <\/p>\n\n\n\n

\"Postupem \u010dasu jsme poc\u00edtili nutnost vyvinout u\u017eivatelsk\u00e9 rozhran\u00ed, kter\u00e9 by je\u0161t\u011b v\u00edce usnadnilo pou\u017e\u00edv\u00e1n\u00ed, a tak bychom mohli software zve\u0159ejnit pro v\u0161echny v\u00fdzkumn\u00e9 pracovn\u00edky, kte\u0159\u00ed by ho pot\u0159ebovali pou\u017e\u00edvat,\" \u0159\u00edk\u00e1 Garcia-Fossa o \u010dl\u00e1nku o softwaru, kter\u00fd si m\u016f\u017eete prohl\u00e9dnout. kliknut\u00edm zde<\/a>.<\/p>\n\n\n\n

Garcia-Fossa tak\u00e9 \u0159\u00edk\u00e1, \u017ee jim chv\u00edli trvalo, ne\u017e ze sn\u00edmk\u016f rozpoznali a ur\u010dili migra\u010dn\u00ed oblast, proto\u017ee sn\u00edmky se mohou od sebe velmi li\u0161it kv\u016fli sv\u011btlu, zaost\u0159en\u00ed a kontrastu, a dnes pou\u017e\u00edvan\u00e1 verze u\u017e dok\u00e1\u017ee analyzovat docela dob\u0159e. <\/p>\n\n\n\n

P\u0159esto na softwaru st\u00e1le pracuj\u00ed a uv\u00e1d\u011bj\u00ed nov\u00e9 a lep\u0161\u00ed verze, proto\u017ee zve\u0159ejn\u011bn\u00fd \u010dl\u00e1nek p\u0159inesl n\u011bkter\u00e9 pot\u0159eby vylep\u0161en\u00ed na z\u00e1klad\u011b popt\u00e1vky u\u017eivatel\u016f.<\/p>\n\n\n\n

Test pou\u017e\u00edvan\u00fd k ov\u011b\u0159en\u00ed v\u00fdkonnosti softwaru, migra\u010dn\u00ed test, test po\u0161kr\u00e1b\u00e1n\u00ed nebo hojen\u00ed ran, je testem b\u011b\u017en\u011b pou\u017e\u00edvan\u00fdm v biologii, proto\u017ee umo\u017e\u0148uje analyzovat z\u00e1kladn\u00ed mechanismus fyziologick\u00fdch a patologick\u00fdch bun\u011b\u010dn\u00fdch d\u011bj\u016f. <\/p>\n\n\n\n

Studium hojen\u00ed ran je vedle angiogeneze a v\u00fdvoje n\u00e1dor\u016f d\u016fle\u017eit\u00fdm zp\u016fsobem, jak porozum\u011bt v\u00fdvoji a modelov\u00e1n\u00ed tk\u00e1n\u00ed. <\/p>\n\n\n\n

Pokud se test prov\u00e1d\u00ed ve dvou rozm\u011brech, je mo\u017en\u00e9 m\u011b\u0159it, jak rychle bu\u0148ky reaguj\u00ed na r\u00e1nu, kter\u00e1 pokr\u00fdv\u00e1 definovanou oblast.<\/p>\n\n\n\n

Jin\u00fdmi slovy, experiment v podstat\u011b spo\u010d\u00edv\u00e1 v tom, \u017ee se v monovrstv\u011b konfluen\u010dn\u00edch bun\u011bk v desti\u010dce vytvo\u0159\u00ed mezera. <\/p>\n\n\n\n

V pr\u016fb\u011bhu \u010dasu za\u010dnou bu\u0148ky migrovat, aby vyplnily mezeru, a lze m\u011b\u0159it rychlost migrace bun\u011bk. <\/p>\n\n\n\n

K m\u011b\u0159en\u00ed rychlosti migrace bun\u011bk pak pot\u0159ebuj\u00ed z\u00edskat sn\u00edmky, a to celou \u0159adu, co\u017e je zase problematick\u00fd krok anal\u00fdzy, proto\u017ee vy\u017eaduje ru\u010dn\u00ed m\u011b\u0159en\u00ed. <\/p>\n\n\n\n

Na\u0161t\u011bst\u00ed dnes m\u00e1me k dispozici mnoho technologi\u00ed, kter\u00e9 n\u00e1m umo\u017e\u0148uj\u00ed zlep\u0161it a modernizovat na\u0161e analytick\u00e9 postupy a v\u011bdc\u016fm umo\u017e\u0148uj\u00ed p\u0159ijmout lep\u0161\u00ed a personalizovan\u011bj\u0161\u00ed zp\u016fsoby, jak z\u00edskat v\u00fdsledek. <\/p>\n\n\n\n

Stejn\u011b jako to ud\u011blali Garcia-Fossa a Gaal.<\/p>\n\n\n\n

Dnes je mo\u017en\u00e9 naj\u00edt dal\u0161\u00ed komer\u010dn\u00ed i nekomer\u010dn\u00ed n\u00e1stroje pro zpracov\u00e1n\u00ed oblasti r\u00e1ny. <\/p>\n\n\n\n

Nejsou v\u0161ak tak jednoduch\u00e9 jako PyScratch a vy\u017eaduj\u00ed od u\u017eivatele ur\u010ditou \u00farove\u0148 programov\u00e1n\u00ed a tak\u00e9 vy\u017eaduj\u00ed od u\u017eivatele pozornost na pln\u00fd \u00favazek, tak\u017ee anal\u00fdza je n\u00e1chyln\u011bj\u0161\u00ed k lidsk\u00fdm chyb\u00e1m, a nav\u00edc \u010das, kter\u00fd v\u00fdzkumn\u00edk pot\u0159ebuje k anal\u00fdze v\u0161ech obr\u00e1zk\u016f a dat.<\/p>\n\n\n\n

V \u010dl\u00e1nku auto\u0159i vysv\u011btluj\u00ed, jak tento software funguje. Ze v\u0161ech sn\u00edmk\u016f po\u0159\u00edzen\u00fdch v r\u00e1mci experimentu z\u00edsk\u00e1 u\u017eivatel soubor s \u010d\u00e1rkou odd\u011blen\u00fdmi hodnotami (.cvs), v\u00fdstup, kter\u00fd uchov\u00e1v\u00e1 tabulkov\u00e1 data v prost\u00e9m textu. <\/p>\n\n\n\n

U\u017eivatel pak m\u016f\u017ee data zpracov\u00e1vat obvykl\u00fdm zp\u016fsobem. Garcia-Fossa \u0159\u00edk\u00e1, \u017ee program byl nezbytn\u00fd pro jej\u00ed magisterskou pr\u00e1ci: \"Software transformuje vstupn\u00ed data na hodnoty, kter\u00e9 d\u00e1vaj\u00ed biologick\u00fd smysl, nap\u0159\u00edklad rychlost migrace bun\u011bk. <\/p>\n\n\n\n

D\u00edky PyScratch jsem mohl l\u00e9pe analyzovat \u00fa\u010dinek sv\u00e9 nano\u010d\u00e1stice na bu\u0148ky rakoviny prostaty a m\u011b\u0159it rychlost migrace bun\u011bk a p\u0159esn\u00fd \u010das, za kter\u00fd se dob\u0159e uzav\u0159ou.\"<\/p>\n\n\n\n

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

Pokud si chcete PyScratch vyzkou\u0161et pro sv\u016fj v\u00fdzkum, software je voln\u011b dostupn\u00fd a ka\u017ed\u00fd z v\u011bdeck\u00e9 komunity jej m\u016f\u017ee pou\u017e\u00edvat, co\u017e pom\u00e1h\u00e1 Garciovi-Fossovi a Gaalovi program vylep\u0161ovat a zdokonalovat.<\/p>\n\n\n\n

 ____<\/p>\n\n\n\n

Jak\u00e9 jsou va\u0161e dosavadn\u00ed zku\u0161enosti s Mind the Graph? Pomozte n\u00e1m zlep\u0161it na\u0161i platformu pro v\u00e1s i pro mnoho dal\u0161\u00edch v\u011bdc\u016f t\u00edm, \u017ee nap\u00ed\u0161ete recenzi Mind the Graph. Napi\u0161te n\u00e1m o sv\u00fdch zku\u0161enostech, sta\u010d\u00ed kliknout na zde<\/a>. <\/p>","protected":false},"excerpt":{"rendered":"

PyScratch je nov\u00fd open-source software implementovan\u00fd v jazyce Python pro anal\u00fdzu migra\u010dn\u00edch dat s u\u017eivatelsky p\u0159\u00edv\u011btiv\u00fdm rozhran\u00edm, kter\u00e9 umo\u017e\u0148uje v\u011bdc\u016fm s minim\u00e1ln\u00edmi nebo \u017e\u00e1dn\u00fdmi program\u00e1torsk\u00fdmi dovednostmi jej pou\u017e\u00edvat. Software byl navr\u017een ve spolupr\u00e1ci t\u0159\u00ed brazilsk\u00fdch v\u011bdc\u016f v laborato\u0159i NanoCell Interactions na univerzit\u011b v Campinas v roce 2017. Byl vytvo\u0159en na z\u00e1klad\u011b [...]<\/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\/cs\/saggi-pyscratch-spatial-and-temporal-information-from-scratch\/\" \/>\n<meta property=\"og:locale\" content=\"cs_CZ\" \/>\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 to know what PyScratch is and how that new tool processes spatial and temporal information from scratch assays.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/mindthegraph.com\/blog\/cs\/saggi-pyscratch-spatial-and-temporal-information-from-scratch\/\" \/>\n<meta property=\"og:site_name\" content=\"Mind the Graph Blog\" \/>\n<meta property=\"article:published_time\" content=\"2021-01-13T11:30:00+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2022-10-18T11:09:26+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/mindthegraph.com\/blog\/wp-content\/uploads\/2021\/01\/pyscratch-a-new-tool-to-process-spatial-and-temporal-information-from-scratch-assays.png\" \/>\n\t<meta property=\"og:image:width\" content=\"1123\" \/>\n\t<meta property=\"og:image:height\" content=\"612\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/png\" \/>\n<meta name=\"author\" content=\"Fabricio Pamplona\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Fabricio Pamplona\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"5 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"A new tool for processing spatial and temporal information","description":"Read this blog to know what PyScratch is and how that new tool processes spatial and temporal information from scratch assays.","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/mindthegraph.com\/blog\/cs\/saggi-pyscratch-spatial-and-temporal-information-from-scratch\/","og_locale":"cs_CZ","og_type":"article","og_title":"A new tool for processing spatial and temporal information","og_description":"Read this blog to know what PyScratch is and how that new tool processes spatial and temporal information from scratch assays.","og_url":"https:\/\/mindthegraph.com\/blog\/cs\/saggi-pyscratch-spatial-and-temporal-information-from-scratch\/","og_site_name":"Mind the Graph Blog","article_published_time":"2021-01-13T11:30:00+00:00","article_modified_time":"2022-10-18T11:09:26+00:00","og_image":[{"width":1123,"height":612,"url":"https:\/\/mindthegraph.com\/blog\/wp-content\/uploads\/2021\/01\/pyscratch-a-new-tool-to-process-spatial-and-temporal-information-from-scratch-assays.png","type":"image\/png"}],"author":"Fabricio Pamplona","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Fabricio Pamplona","Est. reading time":"5 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"WebPage","@id":"https:\/\/mindthegraph.com\/blog\/it\/saggi-pyscratch-spatial-and-temporal-information-from-scratch\/","url":"https:\/\/mindthegraph.com\/blog\/it\/saggi-pyscratch-spatial-and-temporal-information-from-scratch\/","name":"A new tool for processing spatial and temporal information","isPartOf":{"@id":"https:\/\/mindthegraph.com\/blog\/#website"},"datePublished":"2021-01-13T11:30:00+00:00","dateModified":"2022-10-18T11:09:26+00:00","author":{"@id":"https:\/\/mindthegraph.com\/blog\/#\/schema\/person\/c8eaee6d8007ac319523c3ddc98cedd3"},"description":"Read this blog to know what PyScratch is and how that new tool processes spatial and temporal information from scratch assays.","breadcrumb":{"@id":"https:\/\/mindthegraph.com\/blog\/it\/saggi-pyscratch-spatial-and-temporal-information-from-scratch\/#breadcrumb"},"inLanguage":"cs-CZ","potentialAction":[{"@type":"ReadAction","target":["https:\/\/mindthegraph.com\/blog\/it\/saggi-pyscratch-spatial-and-temporal-information-from-scratch\/"]}]},{"@type":"BreadcrumbList","@id":"https:\/\/mindthegraph.com\/blog\/it\/saggi-pyscratch-spatial-and-temporal-information-from-scratch\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/mindthegraph.com\/blog\/"},{"@type":"ListItem","position":2,"name":"PyScratch: A New Tool to Process Spatial and Temporal Information from Scratch Assays"}]},{"@type":"WebSite","@id":"https:\/\/mindthegraph.com\/blog\/#website","url":"https:\/\/mindthegraph.com\/blog\/","name":"Mind the Graph Blog","description":"Your science can be beautiful!","potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/mindthegraph.com\/blog\/?s={search_term_string}"},"query-input":"required name=search_term_string"}],"inLanguage":"cs-CZ"},{"@type":"Person","@id":"https:\/\/mindthegraph.com\/blog\/#\/schema\/person\/c8eaee6d8007ac319523c3ddc98cedd3","name":"Fabricio Pamplona","image":{"@type":"ImageObject","inLanguage":"cs-CZ","@id":"https:\/\/mindthegraph.com\/blog\/#\/schema\/person\/image\/","url":"https:\/\/secure.gravatar.com\/avatar\/da6985d9f20ecb24f3238df103a638ac?s=96&d=mm&r=g","contentUrl":"https:\/\/secure.gravatar.com\/avatar\/da6985d9f20ecb24f3238df103a638ac?s=96&d=mm&r=g","caption":"Fabricio Pamplona"},"description":"Fabricio Pamplona is the founder of Mind the Graph - a tool used by over 400K users in 60 countries. 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\/cs\/author\/fabricio\/"}]}},"_links":{"self":[{"href":"https:\/\/mindthegraph.com\/blog\/cs\/wp-json\/wp\/v2\/posts\/12130"}],"collection":[{"href":"https:\/\/mindthegraph.com\/blog\/cs\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/mindthegraph.com\/blog\/cs\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/mindthegraph.com\/blog\/cs\/wp-json\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/mindthegraph.com\/blog\/cs\/wp-json\/wp\/v2\/comments?post=12130"}],"version-history":[{"count":1,"href":"https:\/\/mindthegraph.com\/blog\/cs\/wp-json\/wp\/v2\/posts\/12130\/revisions"}],"predecessor-version":[{"id":12134,"href":"https:\/\/mindthegraph.com\/blog\/cs\/wp-json\/wp\/v2\/posts\/12130\/revisions\/12134"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/mindthegraph.com\/blog\/cs\/wp-json\/wp\/v2\/media\/12133"}],"wp:attachment":[{"href":"https:\/\/mindthegraph.com\/blog\/cs\/wp-json\/wp\/v2\/media?parent=12130"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/mindthegraph.com\/blog\/cs\/wp-json\/wp\/v2\/categories?post=12130"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/mindthegraph.com\/blog\/cs\/wp-json\/wp\/v2\/tags?post=12130"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}