{"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\/sl\/pyscratch-spatial-and-temporal-information-from-scratch-assays\/","title":{"rendered":"PyScratch: Novo orodje za obdelavo prostorskih in \u010dasovnih informacij iz testov Scratch"},"content":{"rendered":"

PyScratch je nova odprtokodna programska oprema v jeziku Python za analizo migracijskih podatkovnih analiz z uporabniku prijaznim vmesnikom, ki omogo\u010da uporabo znanstvenikom z malo ali ni\u010d znanja programiranja. <\/p>\n\n\n\n

Programska oprema je bila zasnovana v sodelovanju treh brazilskih znanstvenikov v laboratoriju NanoCell Interactions na Univerzi Campinas leta 2017. <\/p>\n\n\n\n

Nastala je iz potrebe teh znanstvenikov, danes pa je namen programske opreme olaj\u0161ati vsakodnevno prakso raziskovalcev, izklju\u010diti ro\u010dno analizo, pove\u010dati ponovljivost in zmanj\u0161ati \u010dlove\u0161ke napake.<\/p>\n\n\n\n

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

Slikovna analiza je eden najpomembnej\u0161ih na\u010dinov, ki ga znanstveniki uporabljajo v razli\u010dnih metodologijah za analizo rezultatov. <\/p>\n\n\n\n

V zadnjih letih se ni pove\u010dala le uporaba avtomatiziranih mikroskopov, temve\u010d tudi kompleksnost pridobljenih podatkov. <\/p>\n\n\n\n

Del znanstvenikovega dela je odkriti, kako ravnati z novo vrsto informacij, poleg tega pa analizirati in obdelovati podatke. <\/p>\n\n\n\n

Za to znanstveniki potrebujejo dobra in specializirana orodja za pravilno pridobivanje in razlago vseh podatkov.<\/p>\n\n\n\n

Program PyScratch je bil prvi\u010d ustvarjen kot pomo\u010d Fernandi Garcia-Fossa, raziskovalki biologinji, pri analizi ogromne koli\u010dine podatkov iz njenih migracijskih testov. <\/p>\n\n\n\n

\"Izvedel sem praskanje rakavih celic in jih 48 ur inkubiral v opremi, pri \u010demer sem vsakih 15 minut posnel slike, na koncu samo enega poskusa pa sem imel pribli\u017eno tiso\u010d slik, ki sem jih lahko pregledal in analiziral! <\/p>\n\n\n\n

To je bilo nemogo\u010de narediti ro\u010dno,\" pravi Garcia-Fossa. Pri re\u0161evanju te te\u017eave je Garcia-Fossa prosila za pomo\u010d svojega partnerja, fizika Vladimirja Gaala, ki se je v tistem \u010dasu u\u010dil Pythona, kar je bila odli\u010dna prilo\u017enost, da to znanje uporabi v praksi.<\/p>\n\n\n\n

Tako sta se oba ukvarjala z re\u0161itvijo prek rutine Python, ki je prepoznala opraskana obmo\u010dja in jih izvozila v datoteko csv. <\/p>\n\n\n\n

\"S\u010dasoma smo za\u010dutili potrebo po razvoju uporabni\u0161kega vmesnika, ki bi omogo\u010dal \u0161e la\u017ejo uporabo, s \u010dimer bi lahko programsko opremo objavili tudi za vse raziskovalce, ki bi jo potrebovali\", pravi Garcia-Fossa o \u010dlanku o programski opremi, ki ga lahko preverite. kliknite tukaj<\/a>.<\/p>\n\n\n\n

Garcia-Fossa tudi pravi, da so potrebovali nekaj \u010dasa, da so na slikah prepoznali in dolo\u010dili obmo\u010dje migracije, saj se slike lahko med seboj zelo razlikujejo zaradi svetlobe, ostrine in kontrasta, razli\u010dica, ki se uporablja danes, pa lahko \u017ee precej dobro analizira. <\/p>\n\n\n\n

Kljub temu \u0161e vedno delajo na programski opremi in uvajajo nove in bolj\u0161e razli\u010dice, saj so v objavljenem \u010dlanku zaradi povpra\u0161evanja uporabnikov izpostavili nekatere potrebe po izbolj\u0161avah.<\/p>\n\n\n\n

Preskus, ki se uporablja za potrjevanje delovanja programske opreme, migracijski preskus, preskus s praskami ali celjenje ran, je preskus, ki se pogosto uporablja v biologiji, saj omogo\u010da analizo osnovnega mehanizma fiziolo\u0161kih in patolo\u0161kih celi\u010dnih dogodkov. <\/p>\n\n\n\n

\u0160tudija celjenja ran je poleg angiogeneze in razvoja tumorjev pomemben na\u010din za razumevanje razvoja in modeliranja tkiv. <\/p>\n\n\n\n

Pri dvodimenzionalnem testu je mogo\u010de izmeriti, kako hitro se celice odzovejo na rano, ki pokriva dolo\u010deno obmo\u010dje.<\/p>\n\n\n\n

Z drugimi besedami, poskus v bistvu pomeni, da v monosloju konfluentnih celic v plo\u0161\u010dici ustvarite vrzel. <\/p>\n\n\n\n

S\u010dasoma se celice za\u010dnejo seliti, da bi zapolnile vrzel, in izmeri se lahko hitrost selitve celic. <\/p>\n\n\n\n

Za merjenje hitrosti migracije celic morajo nato pridobiti ve\u010d slik, kar je problemati\u010den korak analize, saj zahteva ro\u010dno merjenje. <\/p>\n\n\n\n

Na sre\u010do imamo danes na voljo veliko tehnologije za izbolj\u0161anje in nadgradnjo na\u0161ih analiz, ki znanstvenikom omogo\u010da, da sprejmejo bolj\u0161e in bolj prilagojene na\u010dine pridobivanja rezultatov. <\/p>\n\n\n\n

Tako kot Garcia-Fossa in Gaal.<\/p>\n\n\n\n

Danes so na voljo tudi druga komercialna in nekomercialna orodja za obdelavo obmo\u010dja rane. <\/p>\n\n\n\n

Vendar niso tako preprosti kot PyScratch in od uporabnika zahtevajo dolo\u010deno raven programiranja, poleg tega pa od uporabnika zahtevajo stalno pozornost, zaradi \u010desar je analiza bolj dovzetna za \u010dlove\u0161ke napake, poleg \u010dasa, ki ga raziskovalec potrebuje za analizo vseh slik in podatkov.<\/p>\n\n\n\n

V \u010dlanku avtorji pojasnjujejo, kako programska oprema deluje. Iz vseh slik, narejenih v poskusu, uporabnik dobi datoteko z vrednostmi, lo\u010denimi z vejico (.cvs), izhodno datoteko, ki hrani tabelarne podatke v navadnem besedilu. <\/p>\n\n\n\n

Uporabnik lahko nato podatke obdeluje v svojem obi\u010dajnem postopku. Garcia-Fossa pravi, da je bil program bistvenega pomena za njeno magistrsko nalogo: \"Programska oprema pretvori vhodne podatke v vrednosti, ki imajo biolo\u0161ki smisel, kot je hitrost migracije celic. <\/p>\n\n\n\n

Zaradi PyScratcha sem lahko bolje analiziral u\u010dinek svojega nanodelca na celice raka prostate in izmeril hitrost migracije celic ter natan\u010den \u010das dobrega zaprtja.\"<\/p>\n\n\n\n

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

\u010ce \u017eelite PyScratch preizkusiti v svojih raziskavah, je programska oprema prosto dostopna in jo lahko uporablja vsakdo iz znanstvene skupnosti, kar pomaga Garcii-Fossi in Gaalu, da program izbolj\u0161ata in izbolj\u0161ata.<\/p>\n\n\n\n

 ____<\/p>\n\n\n\n

Kak\u0161ne so va\u0161e dosedanje izku\u0161nje s storitvijo Mind the Graph? Pomagajte nam izbolj\u0161ati na\u0161o platformo za vas in \u0161tevilne druge znanstvenike z objavo ocene Mind the Graph. Povejte nam o svojih izku\u0161njah, samo kliknite tukaj<\/a>. <\/p>","protected":false},"excerpt":{"rendered":"

PyScratch je nova odprtokodna programska oprema v jeziku Python za analizo migracijskih podatkovnih analiz z uporabniku prijaznim vmesnikom, ki omogo\u010da uporabo znanstvenikom z malo ali ni\u010d znanja programiranja. Programska oprema je bila zasnovana v sodelovanju treh brazilskih znanstvenikov v laboratoriju NanoCell Interactions na Univerzi Campinas leta 2017. Narejena je bila v [...]<\/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\/sl\/saggi-pyscratch-spatial-and-temporal-information-from-scratch\/\" \/>\n<meta property=\"og:locale\" content=\"sl_SI\" \/>\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\" 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