{"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\/sv_se\/pyscratch-spatial-och-temporal-information-fran-scratch-assays\/","title":{"rendered":"PyScratch: Ett nytt verktyg f\u00f6r att bearbeta rumslig och tidsm\u00e4ssig information fr\u00e5n Scratch Assays"},"content":{"rendered":"

PyScratch \u00e4r en ny programvara med \u00f6ppen k\u00e4llkod som implementerats i Python f\u00f6r analys av migrationsdata, med ett anv\u00e4ndarv\u00e4nligt gr\u00e4nssnitt som g\u00f6r det m\u00f6jligt f\u00f6r forskare med f\u00e5 eller inga programmeringskunskaper att anv\u00e4nda det. <\/p>\n\n\n\n

Programvaran utformades 2017 i ett samarbete mellan tre brasilianska forskare i NanoCell Interactions-laboratoriet vid universitetet i Campinas. <\/p>\n\n\n\n

Den f\u00f6ddes ur dessa forskares behov, och idag \u00e4r programvarans syfte att underl\u00e4tta forskarnas dagliga arbete, utesluta manuell analys, \u00f6ka reproducerbarheten och minimera m\u00e4nskliga fel.<\/p>\n\n\n\n

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

Bildanalys har varit ett av de viktigaste s\u00e4tten f\u00f6r forskare att analysera resultat med hj\u00e4lp av olika metoder. <\/p>\n\n\n\n

Inte bara anv\u00e4ndningen av automatiserade mikroskop har \u00f6kat under de senaste \u00e5ren, utan \u00e4ven komplexiteten i de data som samlas in. <\/p>\n\n\n\n

En del av en forskares jobb \u00e4r att ta reda p\u00e5 hur man ska hantera en ny typ av information, och dessutom analysera och bearbeta data. <\/p>\n\n\n\n

F\u00f6r att detta ska vara m\u00f6jligt beh\u00f6ver forskarna bra och specialiserade verktyg f\u00f6r att korrekt extrahera och tolka alla data.<\/p>\n\n\n\n

PyScratch skapades f\u00f6rst f\u00f6r att hj\u00e4lpa Fernanda Garcia-Fossa, en biologforskare, att analysera en enorm m\u00e4ngd data fr\u00e5n sina migrationsanalyser. <\/p>\n\n\n\n

\"Jag skrapade cancercellerna och inkuberade dem i utrustningen under 48 timmar, tog bilder var 15:e minut och i slutet av ett enda experiment hade jag ungef\u00e4r tusen bilder att titta p\u00e5 och analysera! <\/p>\n\n\n\n

Det var om\u00f6jligt att g\u00f6ra det manuellt\", s\u00e4ger Garcia-Fossa. F\u00f6r att l\u00f6sa det problemet tog Garcia-Fossa hj\u00e4lp av sin partner, fysikern Vladimir Gaal, som just d\u00e5 h\u00f6ll p\u00e5 att l\u00e4ra sig Python, vilket var ett utm\u00e4rkt tillf\u00e4lle att oms\u00e4tta den kunskapen i praktiken.<\/p>\n\n\n\n

S\u00e5 de b\u00e5da arbetade med l\u00f6sningen genom en Python-rutin, som k\u00e4nde igen de repade omr\u00e5dena och exporterade till en csv-fil. <\/p>\n\n\n\n

\"Med tiden k\u00e4nde vi oss tvungna att utveckla ett anv\u00e4ndargr\u00e4nssnitt som g\u00f6r det \u00e4nnu enklare att anv\u00e4nda, p\u00e5 det s\u00e4ttet kunde vi publicera programvaran f\u00f6r alla forskare som ocks\u00e5 beh\u00f6vde anv\u00e4nda den\", s\u00e4ger Garcia-Fossa om artikeln om programvaran som du kan kolla in klicka h\u00e4r<\/a>.<\/p>\n\n\n\n

Garcia-Fossa ber\u00e4ttar ocks\u00e5 att det tog ett tag att k\u00e4nna igen och definiera migrationsomr\u00e5det fr\u00e5n bilderna eftersom bilderna kan skilja sig mycket fr\u00e5n varandra p\u00e5 grund av ljus, fokus och kontrast, och den version som anv\u00e4nds idag kan redan analysera ganska bra. <\/p>\n\n\n\n

De arbetar dock fortfarande med att lansera nya och b\u00e4ttre versioner av programvaran, eftersom den publicerade artikeln har tagit upp vissa f\u00f6rb\u00e4ttringsbehov p\u00e5 grund av anv\u00e4ndarnas efterfr\u00e5gan.<\/p>\n\n\n\n

Det assay som anv\u00e4nds f\u00f6r att validera programvarans prestanda, migrationsassay, scratch assay eller s\u00e5rl\u00e4kning, \u00e4r ett assay som ofta anv\u00e4nds inom biologi eftersom det g\u00f6r det m\u00f6jligt att analysera den underliggande mekanismen f\u00f6r fysiologiska och patologiska cellul\u00e4ra h\u00e4ndelser. <\/p>\n\n\n\n

Att studera s\u00e5rl\u00e4kning \u00e4r ett viktigt s\u00e4tt att f\u00f6rst\u00e5 utveckling och v\u00e4vnadsmodellering, f\u00f6rutom angiogenes och tum\u00f6rutveckling. <\/p>\n\n\n\n

N\u00e4r analysen utf\u00f6rs i tv\u00e5 dimensioner \u00e4r det m\u00f6jligt att m\u00e4ta hur snabbt cellerna reagerar p\u00e5 s\u00e5ret och t\u00e4cker det definierade omr\u00e5det.<\/p>\n\n\n\n

Med andra ord \u00e4r experimentet i princip att skapa ett gap i monolagret av konfluenta celler i en plack. <\/p>\n\n\n\n

Med tiden b\u00f6rjar cellerna migrera f\u00f6r att fylla gapet, och hastigheten f\u00f6r cellernas migration kan m\u00e4tas. <\/p>\n\n\n\n

F\u00f6r att m\u00e4ta cellmigrationshastigheten m\u00e5ste de sedan ta bilder, massor av bilder, vilket i sin tur \u00e4r ett problematiskt steg i analysen eftersom det kr\u00e4ver manuell m\u00e4tning. <\/p>\n\n\n\n

Lyckligtvis har vi idag tillg\u00e5ng till en hel del teknik som kan f\u00f6rb\u00e4ttra och uppgradera v\u00e5r analyspipeline, s\u00e5 att forskare kan anv\u00e4nda b\u00e4ttre och mer personliga s\u00e4tt att f\u00e5 fram ett resultat. <\/p>\n\n\n\n

Som Garcia-Fossa och Gaal gjorde det.<\/p>\n\n\n\n

Idag \u00e4r det m\u00f6jligt att hitta andra kommersiella och icke-kommersiella verktyg f\u00f6r att bearbeta s\u00e5romr\u00e5det. <\/p>\n\n\n\n

Men de \u00e4r inte lika enkla som PyScratch, och kr\u00e4ver av anv\u00e4ndaren en viss niv\u00e5 av programmering och kr\u00e4ver ocks\u00e5 heltid uppm\u00e4rksamhet fr\u00e5n anv\u00e4ndaren, vilket g\u00f6r analysen mer mottaglig f\u00f6r m\u00e4nskliga fel, plus den tid som forskaren tar f\u00f6r att analysera alla bilder och data.<\/p>\n\n\n\n

I artikeln f\u00f6rklarar f\u00f6rfattarna hur programvaran fungerar. Fr\u00e5n alla bilder som tagits i experimentet f\u00e5r anv\u00e4ndaren en kommaseparerade v\u00e4rden-fil (.cvs), en fil som lagrar tabelldata i klartext. <\/p>\n\n\n\n

Anv\u00e4ndaren kan sedan bearbeta data i sin vanliga rutin. Garcia-Fossa s\u00e4ger att programmet var avg\u00f6rande f\u00f6r hennes magisteruppsats: \"Programvaran omvandlar indata till v\u00e4rden som \u00e4r biologiskt meningsfulla, till exempel cellmigrationshastighet. <\/p>\n\n\n\n

Jag kunde b\u00e4ttre analysera effekten av min nanopartikel p\u00e5 prostatacancerceller och m\u00e4ta cellmigrationshastigheten och den exakta tiden f\u00f6r det goda avslutet, allt tack vare PyScratch.\"<\/p>\n\n\n\n

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

Om du vill prova PyScratch f\u00f6r din forskning \u00e4r programvaran fritt tillg\u00e4nglig och alla inom forskarv\u00e4rlden f\u00e5r anv\u00e4nda den, vilket hj\u00e4lper Garcia-Fossa och Gaal att utveckla och f\u00f6rb\u00e4ttra programmet.<\/p>\n\n\n\n

 ____<\/p>\n\n\n\n

Hur \u00e4r din erfarenhet av Mind the Graph hittills? Hj\u00e4lp oss att f\u00f6rb\u00e4ttra v\u00e5r plattform f\u00f6r dig och f\u00f6r m\u00e5nga andra forskare genom att skriva en Mind the Graph-recension. Ber\u00e4tta f\u00f6r oss om din upplevelse, klicka bara p\u00e5 h\u00e4r<\/a>. <\/p>","protected":false},"excerpt":{"rendered":"

PyScratch \u00e4r en ny programvara med \u00f6ppen k\u00e4llkod som implementerats i Python f\u00f6r analys av migrationsdata, med ett anv\u00e4ndarv\u00e4nligt gr\u00e4nssnitt som g\u00f6r det m\u00f6jligt f\u00f6r forskare med f\u00e5 eller inga programmeringskunskaper att anv\u00e4nda den. Programvaran utformades i ett samarbete mellan tre brasilianska forskare i NanoCell Interactions-laboratoriet vid University of Campinas 2017. Det var [...]<\/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\/sv_se\/saggi-pyscratch-spatial-and-temporal-information-from-scratch\/\" \/>\n<meta property=\"og:locale\" content=\"sv_SE\" \/>\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 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