Automatic cell counter for cell viability estimation

Despite several methods that exist in different fields of life sciences, certain biotechnological applications still require microscopic analysis of the samples and in many instances, counting of cells. Some of those are drug delivery, transfection or analysis of mechanism fluorescent probes are used to detect cell viability, efficiency of a specific drug delivery or some other effect. For analysis and quantification of these results it is necessary to either manually or automatically count and analyze microscope images. However, in everyday use many researchers still count cells manually since existing solutions require either some specific knowledge of computer vision and/or manual fine tuning of various parameters. Here we present a new software solution (named CellCounter) for automatic and semi-automatic cell counting of fluorescent microscopic images. This application is specifically designed for counting fluorescently stained cells. The program enables counting of cell nuclei or cell cytoplasm stained with different fluorescent stained. This simplifies image analysis for several biotechnological applications where fluorescent microscopy is used. We present results and validate the presented automatic cell counting program for cell viability application. We give empirical results showing the efficiency of the proposed solution by comparing manual counts with the results returned by automated counting. We also show how the results can be further improved by combining manual and automated

Automatic cell counter for cell viability estimation

Despite several methods that exist in different fields of life sciences, certain biotechnological applications still require microscopic analysis of the samples and in many instances, counting of cells. Some of those are drug delivery, transfection or analysis of mechanism fluorescent probes are used to detect cell viability, efficiency of a specific drug delivery or some other effect. For analysis and quantification of these results it is necessary to either manually or automatically count and analyze microscope images. However, in everyday use many researchers still count cells manually since existing solutions require either some specific knowledge of computer vision and/or manual fine tuning of various parameters. Here we present a new software solution (named CellCounter) for automatic and semi-automatic cell counting of fluorescent microscopic images. This application is specifically designed for counting fluorescently stained cells. The program enables counting of cell nuclei or cell cytoplasm stained with different fluorescent stained. This simplifies image analysis for several biotechnological applications where fluorescent microscopy is used. We present results and validate the presented automatic cell counting program for cell viability application. We give empirical results showing the efficiency of the proposed solution by comparing manual counts with the results returned by automated counting. We also show how the results can be further improved by combining manual and automated

Automatic adaptation of filter sequences for cell counting

Manual cell counting in microscopic images is usually tedious, time consuming and prone to human error. Several programs for automatic cell counting have been developed so far, but most of them demand some specific knowledge of image analysis and/or manual fine tuning of various parameters. Even if a set of filters is found and fine tuned to the specific application, small changes to the image attributes might make the automatic counter very unreliable. The goal of this article is to present a new application that overcomes this problem by learning the set of parameters for each application, thus making it more robust to changes in the input images. The users must provide only a small representative subset of images and their manual count, and the program offers a set of automatic counters learned from the given input. The user can check the counters and choose the most suitable one. The resulting application (which we call Learn123) is specifically tailored to the practitioners, i.e. even though the typical workflow is more complex, the application is easy to use for non-technical experts

Comparison of two automatic cell-counting solutions for fluorescent microscopic images

Cell counting in microscopic images is one of the fundamental analysis tools in life sciences, but is usually tedious, time consuming and prone to human error. Several programs for automatic cell countinghavebeendeveloped sofar,butmostof them demand additional training or data input from the user. Most of them do not allow the users to online monitor the counting results, either. Therefore, we designed two straightforward, simple-to-use cell-counting programs that also allow users to correct the detection results. In this paper, we present the CELLCOUNTER and LEARN123 programs for automatic and semiautomatic counting of objects in fluorescent microscopic images (cells or cell nuclei) with a user-friendly interface. Although CELLCOUNTER is based on predefined and fine-tuned set of filters optimized on sets of chosen experiments, LEARN123 uses an evolutionary algorithm to determine the adapt filter parameters based on a learning set of images. CELLCOUNTER also includes an extension for analysis of overlaying images. The efficiency of both programs was assessed on images of cells stained with different fluorescent dyes by comparing automatically obtained results with results that were manually annotated by an expert. With both programs, the correlation between automatic and manual counting was very high (R2 < 0.9), although CELLCOUNTER had some difficulties processing images with no cells or weakly stained cells, where sometimes the background noise was recognized as an object of interest. Nevertheless, the differences between manual and automatic counting were small compared to variations between experimental repeats. Both programs significantly reduced the time required to process the acquired images from hours tominutes. The programs enable consistent, robust, fast and accurate detection of fluorescent objects and can therefore be applied to a range of different applications in different fields of life sciences where fluorescent labelling is used for quantification of various phenomena. Moreover, CELLCOUNTER overlay extension also enables fast analysis of related images thatwouldotherwise require imagemergingforaccurateanalysis, whereas LEARN123’s evolutionary algorithm can adapt counting parameters to specific sets of images of different experimental settings

Automatic adaptation of filter sequences for cell counting

Manual cell counting in microscopic images is usually tedious, time consuming and prone to human error. Several programs for automatic cell counting have been developed so far, but most of them demand some specific knowledge of image analysis and/or manual fine tuning of various parameters. Even if a set of filters is found and fine tuned to the specific application, small changes to the image attributes might make the automatic counter very unreliable. The goal of this article is to present a new application that overcomes this problem by learning the set of parameters for each application, thus making it more robust to changes in the input images. The users must provide only a small representative subset of images and their manual count, and the program offers a set of automatic counters learned from the given input. The user can check the counters and choose the most suitable one. The resulting application (which we call Learn123) is specifically tailored to the practitioners, i.e. even though the typical workflow is more complex, the application is easy to use for non-technical experts

An algorithm for the automatic identification of the key points in head soft tissues

The scope of this BSc thesis is to describe the algorithm that traces the soft tissue silhouette of a face on STRGV image (skull lateral X-ray) and then locates key points of soft tissue like tip of the nose, chin and soft tissue nasion. In order to make an informed decision on orthodontic treatment or orthognatic surgery, dentists- orthodontist and dental surgeons use various tools. This tools provide relevant information for diagnosis and help establish an appropriate treatment plan. Goals of the treatment are functional and aestethic improvements. Cephalometric analyses are one of these tools. The goal of this thesis is to find the most appropriate methodology for automatic recognition of key reference points on soft tissue of the head in order to simplify and speed up the process of creating cephalometric analyses in AxCeph software [1]

Pomen knjižnic za izobraževanje odraslih

In February and March 1997, an inquiry was undertaken at » Delavska knjižnica« in Ljubljana, a department of »Knjižnica Otona Župančiča«, and at »Središče za samostojno učenje pri Šolskem centru za pošto, ekonomiko in telekomunikacije«, with the ain of gaining some kno­ wledge about how adults take part in self­ education or learning, how freguently they visit libraries or similar institutions and how these institutions, could help them in this respect. The results and the analysis of both inquiries are presented.V Delavski kniižnici v Ljubljani, enoti Knjižnice Otona Zupančiča, ter v Središču za samostojno učenje pri Šolskem centru za pošto, ekonomiko in telekomunikacije sta bili v februarju in marcu leta 1997 izvedeni manjši anketi, ki naj bi na omejenem vzorcu preverili, koliko in kako se odrasli izobražujejo ali učijo, ali v ta namen obiskujejo knjižnico oziroma druge podobne institucije in s katerimi oblikami bi jim te institucije pri tem lahko pomagale. Predstavljeni so rezultati obeh anket in njihova analiza

An algorithm for the automatic identification of the key points in head soft tissues

The scope of this BSc thesis is to describe the algorithm that traces the soft tissue silhouette of a face on STRGV image (skull lateral X-ray) and then locates key points of soft tissue like tip of the nose, chin and soft tissue nasion. In order to make an informed decision on orthodontic treatment or orthognatic surgery, dentists- orthodontist and dental surgeons use various tools. This tools provide relevant information for diagnosis and help establish an appropriate treatment plan. Goals of the treatment are functional and aestethic improvements. Cephalometric analyses are one of these tools. The goal of this thesis is to find the most appropriate methodology for automatic recognition of key reference points on soft tissue of the head in order to simplify and speed up the process of creating cephalometric analyses in AxCeph software [1]

Multi-storey timber structures

Skozi zgodovino se je razvilo veliko nosilnih sistemov lesenih konstrukcij. Najbolj pogosti so: kladna ali brunasta nosilna konstrukcija, predalčna nosilna konstrukcija, stebrna nosilna konstrukcija, okvirna nosilna konstrukcija, panelna nosilna konstrukcija in masivna nosilna konstrukcija. Pri gradnji večetažnih stavb pa se najpogosteje uporabljajo okvirna, panelna ter masivna nosilna konstrukcija. Na podlagi raznih raziskav so na svetu zgradili že veliko število večetažnih lesenih stavb. Predstavila sem nekaj zanimivejših: Murray Grove Tower, The Tree, Hoho tower in Tamedia. V Sloveniji je delež lesenih novogradenj glede na naravne danosti še vedno majhen. Glavni razlog tega je slabše poznavanje sodobne napredne gradnje. Tu skoraj ne najdemo večetažne stavbe, saj Slovenija spada med potresno ogrožene države in vpliv potresne obtežbe na lesene konstrukcije še ni povsem raziskan. Opisala sem poslovno stavbo Eltima in skladišče Ekoprodukt. Kar nekaj slovenskih podjetij se je v preteklosti ukvarjalo z izgradnjo večetažnih lesenih konstrukcij pri nas ali v tujini. Nekatere sem predstavila tudi v nalogi.In the past many loadbearing systems in timber construction has been developed. The basic systems are: log construction, timber-frame construction, balloon-frame and platform-frame construction, panel construction, frame construction nad solid timber construction. For multistorey timber buildings are preferred: frame construction, panel construction and timber solid construction. Based on many research, a large numer of multi-storey timber construction has been built. I presented some of them: Murray Grove Tower, The Tree, Hoho tower and Tamedia.Slovenia has not many new buildings made of wood, according to forestation. The main reason for that is lack of knowledge of advanced timber construction. Also it has very little multi-storey timber construction, because it belong to coutries with high seismic threat and seismic loadbearing of timber construction has not been explored yet. I have presented office building Eltima and storehouse Ekoprodukt. Many slovenian companies have participated in construction of multi-storey timber buildings. Some of them i presented in this thesis

Ko pri pouku slovenščine »vidim vse zvezde«

Kot primer dobre prakse predstavljamo 90-minutno učno enoto s tematskega področja vesolje za študente in študentke slovenščine kot tujega jezika na izpopolnjevalni ravni z vključitvijo vseh štirih jezikovnih kompetenc: branja, poslušanja, govorjenja in pisanja. S tem dopolnjujemo leksikalno poznavanje enega od strokovnih področij, ki ni zajeto v obstoječe učbenike Centra za slovenščino kot drugi in tuji jezik. Pri izbiri leksike se opiramo na seznam besed in predvsem besednih zvez iz poglavja Vesolje v Tematskem slovarju češčine, slovenščine in makedonščine, ki je leta 2021 izšel na Masarykovi univerzi v Brnu (Tematický slovník češtiny, slovinštiny a makedonštiny). V učni enoti se osredotočamo predvsem na stalne besedne zveze in tipične kolokacije, njihovo rabo pa preverjamo s pomočjo slovarjev (portal Fran.si, spletni Kolokacijski slovar sodobne slovenščine), besedil in posnetka. Študentje in študentke spoznajo nekaj frazeoloških enot s kozmičnimi sestavinami, omenimo pa tudi kratek izbor znanih slovenskih glasbenih in književnih del, v katerih se že v naslovu pojavljajo besede, povezane s temo. Cilj učne enote je, da študent ali študentka razume osnovne strokovne pojme s področja vesolja pri branju in poslušanju ter jih pisno in ustno ustrezno uporablja