ARIS - User contributions [en]

ARIS:About

2024-01-18T11:07:38Z

Patricia:

<languages/>
<translate>


ARIS is a laboratory software system for the management and analysis of data related to patients, requests, diagnoses and analytical tests. It offers basic functionality and a simple interface that can be flexibly configured to support the main tasks of a laboratory.


ARIS has been developed by the [https://www.fundacionprobitas.org/en/home ''Fundació Probitas''] and the [http://www.upc.edu ''Universitat Politècnica de Catalunya'' (UPC)], and is available to laboratories free of charge.

{|
| [[File:LogoProbitas.png|250px|link=https://www.fundacionprobitas.org/en/home]]
| [https://www.fundacionprobitas.org/en/home ''Fundació Probitas''] contributes to improve the health of the most vulnerable populations, strengthening the capacities of the public health system in collaboration with entities in recipient countries and with global bodies working in international aid to support development.
|-
| [[File:LogoUPC.png|250px|link=http://www.upc.edu]]
| [http://www.upc.edu ''Universitat Politècnica de Catalunya'' (UPC)] is a public institution of research and higher education in the fields of engineering, architecture, science and technology. Its mission is to contribute to the construction of a sustainable and fair world, through research, technology transfer, dissemination of knowledge and training of professionals.
|}

The use of this program is governed by the Terms and conditions that the user has accepted at the time of requesting the download of the program to the Fundación Probitas. The software respects the terms and conditions of the licenses of the open source software (copyleft) used in its development: [https://www.python.org Python], [https://nodejs.org Node.js], [https://www.sqlite.org SQLite], and [https://github.com/ultralytics/yolov5 YOLOv5].

Licensed under the [https://joinup.ec.europa.eu/collection/eupl/eupl-text-eupl-12 EUPL-1.2-or-later].

</translate>

Main Page

2023-10-04T14:57:22Z

Patricia:

<languages/>
<translate>

[[Category:Main Page]]


<p style="font-size:24px;"><strong>IMAGING: For an improvement of Health through rapid, reliable and economic diagnosis</strong></p>


[[File:Imaging-overview.png|400px|right|frame|Imaging Overview]]


The [[Global Laboratory Initiative]] (GLI) is a program set up by the [https://www.fundacionprobitas.org/en/home Probitas Foundation] in 2010 with the aim of reinforcing the capacities of clinical diagnostic laboratories in the most vulnerable regions of the world.
As part of this big initiative Probitas promoted an [https://imaging.upc.edu/en initiative to create a platform to automate the diagnosis of Malaria and Neglected tropical diseases (NTDs)]. This pages contain information describing different hardware and software technologies involved in this project.


__TOC__

== <span id="ARIS"></span>Analytical requests information system (ARIS) == 
[[ARIS:main|ARIS]] is a laboratory software system for managing and analyzing data related to patients, requests, diagnostics, and analytical tests.
It offers basic functionalities and a simple interface that can be flexibly configured to support the main tasks of a laboratory.

== Robotized microscope == 
[[Microscope:Main|Robotized microscope]] is a set of 3D hardware pieces connected to an Arduino engine that automate the image capture from samples.
A mobile phone controls the movement of the plaque, and eventually get the images of the sample.

=== Mobile App === 
The [[MobileApp:Main|Mobile App]] is an open source software application to control the Arduino engines that move the plaque and focus the ocular of the microscope, as well as automatically take pictures of the sample.
Eventually, the images taken with the app can be downloaded to the desktop application [[ARIS:main|ARIS]].

== Annotation App == 
The [[AnnotationApp:Main|Annotation App]] is a software tool facilitating the annotation of images to create training datasets.
Given an image of a sample, it allows to frame an object and indicate whether it is leucocyte, parasite, etc.
Eventually, once we have enough tagged images, these are used to train a Neural Network that can automate the process with high precision.

== Annotated images Data Lake == 
The [[DataLake:Main|Data Lake]] is a repository of images with their corresponding annotations.
This include the management software, as well as the necessary tools to extract some basic statistics and easily download subsets of images that can be used as a training set for Machine Learning.

</translate>

Configuration

2023-09-21T10:11:26Z

Patricia:

[[Category:ARIS:Configuration]]
<div style="float:right; margin: 0px 0px 0px 0px">
<graphviz border='frame' format='svg'>
digraph ConfigurationDiagram {
nodesep=0.05;
node [shape=oval style=filled fillcolor=orange fontsize="9pt" margin="0.01, 0.01"];

Configuration [label="Configuration"];
ConfGeneric [label="Generic", URL="#Generic_configuration"];
ConfTechnical [label="Technical", URL="#Technical_configuration"];

Configuration -> ConfGeneric;
Configuration -> ConfTechnical;

Regions [label="Regions", shape=tab, URL="#Generic_configuration"];
Locations [label="Locations", shape=tab, URL="#Generic_configuration"];
Units [label="Units", shape=tab, URL="#Generic_configuration"];
HealthFacilities [label="Health, Facilities" shape=tab, URL="#Generic_configuration"];
Physicians [label="Physicians", shape=tab, URL="#Generic_configuration"];
Gender [label="Gender", shape=tab, URL="#Generic_configuration"];
IdentificationCards [label="Identification Cards", shape=tab, URL="#Generic_configuration"];
StateOfTheRequest [label="State of the Request", shape=tab URL="#State_of_the_request"];

ConfGeneric -> Regions;
ConfGeneric -> Locations;
ConfGeneric -> Units;
ConfGeneric -> HealthFacilities;
ConfGeneric -> Physicians;
ConfGeneric -> Gender;
ConfGeneric -> IdentificationCards;
ConfGeneric -> StateOfTheRequest;

LaboratoryAreas [label="Laboratory Areas", shape=tab, URL="#Technical_configuration"];
AnalyticalTests [label="Analytical Tests", shape=tab URL="#Analytical_tests"];
AnalyticalTestsGroups [label="Analytical Tests Groups", shape=tab URL="#Analytical_tests_groups"];
AnalyticalProfiles [label="Analytical Profiles", shape=tab URL="#Analytical_profiles"];
KindsOfSamples [label="Kinds of Samples", shape=tab, URL="#Technical_configuration"];
SampleIncidents [label="Sample Incidents", shape=tab, URL="#Technical_configuration"];
SampleOrigins [label="Sample Origins", shape=tab, URL="#Technical_configuration"];
PregnancyPhases [label="Pregnancy Phases", shape=tab, URL="#Technical_configuration"];
DataTypes [label="Datatypes", shape=tab, URL="#Datatypes"];
ReportingOrder [label="Reporting Order", shape=tab, URL="#Reporting_order"];

ConfTechnical -> LaboratoryAreas;
ConfTechnical -> AnalyticalTests;
ConfTechnical -> AnalyticalTestsGroups;
ConfTechnical -> AnalyticalProfiles;
ConfTechnical -> KindsOfSamples;
ConfTechnical -> SampleIncidents;
ConfTechnical -> SampleOrigins;
ConfTechnical -> PregnancyPhases;
ConfTechnical -> DataTypes;
ConfTechnical -> ReportingOrder;

{ rank=same; Regions Units Physicians IdentificationCards LaboratoryAreas AnalyticalTestsGroups KindsOfSamples SampleOrigins DataTypes}
{ rank=same; ConfGeneric ConfTechnical}
{ rank=sink; Locations HealthFacilities Gender StateOfTheRequest AnalyticalTests AnalyticalProfiles SampleIncidents PregnancyPhases ReportingOrder}}
</graphviz>
</div>

__TOC__

The configuration functionality allows the user to manipulate ARIS, adding or changing some of its aspects for a better customization.
These have been divided into two groups, depending on the knowledge needed to use them.
The first group is absolutely generic and any user in the lab should be able to provide the required information.
However, for the second group, more specific biomedical knowledge will be needed.

==Generic configuration==
[[File:Genericconfiguration.PNG|right|600px|thumb|Editing the labels used for the states]]
This form controls the values of all non-free text fields (i.e., those that appear when clicking on an [[ARIS:User Guide#Arrow|arrow]]) within the system. Through each tab, the user is able to create, edit and delete the values of one of these fields.
If the laboratory is not interested in one of the values, but the user does not wish to delete the information from the system, it can be simply disabled, so it will not be shown in the corresponding drop-down menu. This is done by unticking the ''Active'' checkbox. </br> [[File:Activecheckbox.PNG|75px|Activated checkbox]] ⇔ [[File:Deactivatedcheckbox.PNG|75px|Deactivated checkbox]] </br>
List of tabs:
*Regions (initially empty)
*Locations (initially empty)
*Units
*Health Facilities (initially empty)
*Physicians (initially empty)
*Gender
*Identification cards
*State of the request

Some of them also include hierarchical information. Thus, physicians point to health facilities, health facilities point to locations and these to regions. This information is used in the forms to show the right available values depending on the parent choice in the hierarchy.

===State of the request===
From the ''state of the request'' tab, only the ''label'' field can be edited. Notice that this indicates the different phases a request goes through in the application during its lifecycle, and not only a passive value to be stored.

==Technical configuration==
The ''Laboratory areas'', ''Kinds of sample'', ''Sample incidents'', ''Sample origins'' and ''Pregnancy phases'' tabs, have exactly the same effect as the ones under the [[#Generic configuration|generic configuration]] (i.e., they simply provide the available values in drop boxes).
However, the following tabs have further effects in the behaviour of the forms.

===Analytical tests===
[[File:Analyticalprofile.PNG|right|thumb|700px| Editing analytical profiles]]
This is without doubt the most crucial concept in the configuration, since it defines the available kinds of tests in the laboratory.
They are identified by a name, but also contain a code that will always be shown next to the name.
To facilitate the management of the laboratory, kinds of tests are assigned to a laboratory area, which will be used both in the generation of reports for the patients, as well as in the analysis of data regarding the performance of the laboratory itself.

Each kind of test is then related to a kind of sample.
Only after that kind of sample is provided by the patient, the corresponding test will be allowed to have an associated result.

Each test must have a [[#Datatypes|datatype]], which indicates the kind of result it will accept, this being either numerical (integer or real) or enumerate.
For numerical test results, units of the test can be indicated for informative purposes, together with upper and lower bounds of the result can be defined.
These will be automatically checked.
Only results within the declared boundaries will get a green tick next to them.
Those outside the boundaries will be detected and automatically marked with a red cross.
Validating the value will rely anyway on the laboratory supervisor.
However, a note can be provided here to indicate exceptions to the boundaries or any information that is considered relevant to either the technician or the supervisor.

Finally, there are two specific boolean fields:
* Referred → Indicates that an action or test is performed in another hospital. The option marked in the configuration only determines the default of this field for each test. It does not impede the user from choosing differently in the [[ARIS:Requests|Requests]] forms.
* Automatic → Enables the kind of test to be partially automated. The result of the test is not manually obtained by a person, but by an AI. If this option is disabled in the configuration, the user will not be able to mark it otherwise in the [[ARIS:Requests|Requests]] forms. However, if it is enabled, the user will be able to choose if she desires for the test to be done automatically or not in the [[ARIS:Requests|Requests]] forms.

===Analytical tests groups===
In this tab, groups of tests can be formed for a quicker selection when choosing which tests to perform on a patient. When creating or editing a new group, a ''Group Of Tests Information'' form must be filled in or modified. In this form, the group must be given a name and the user must choose the tests included in the group from the box provided. In the left-hand side list, the groups are in alphabetical order and if the user wishes for a quicker option, there is a search bar on top of the box to write down and filter the tests.
Simply clicking on the name of a test adds it to the group, hence appearing in the right-hand side list.

The analytical tests groups are also used to sort the tests in the generated report of a request.

===Analytical profiles===
In this tab, profiles of tests can be formed for a quicker selection when choosing which groups of tests or individual tests to perform on a patient.
When creating or editing a new profile, an ''Analytical Profile Information'' form must be filled in or modified.
In this form, the profile must be given a name and the user must choose the tests and the groups included in the profile from the lists provided.
The groups and tests are in alphabetical order and if the user wishes for a quicker option, there is a search bar on top of the box to write down and filter the tests and groups.

Choosing a group selects in the corresponding list all the tests belonging to it.
Then, these cannot be individually removed from the profile, but only by removing the group.
Moreover, a test added later to the group will automatically appear as part of any profile containing that group, which is indicated by a lock icon next to the test name.

Analytical profiles do not have any effect in the report generated for a request.

===Datatypes===

Enumerate datatypes can be defined here (integer and real numbers are always available).
These are simply lists of potential results that can be used in any kind of test.

===Reporting order===
[[File:Reportingorder.PNG|Centre|500px|thumb|Editing the laboratory areas order from the reporting areas tab]]
This tab allows ordering the elements in the PDF worklist and in the report of a request.
The tests appearing in them will be firstly sorted by laboratory area, then groups of tests, and finally individual tests.
This is done by choosing one of the three elements, which will lead to another form with a list and two vertical arrows on the left side of the image.
Any number of elements can be simultaneously selected by simply clicking on them.
Then, the arrows will allow to move them up or down in the list, and hence in the generated PDF documents.

Configuration

2023-09-19T14:45:41Z

Patricia:

[[Category:ARIS:Configuration]]
<div style="float:right; margin: 0px 0px 0px 0px">
<graphviz border='frame' format='svg'>
digraph ConfigurationDiagram {
nodesep=0.05;
node [shape=oval style=filled fillcolor=orange fontsize="9pt" margin="0.01, 0.01"];

Configuration [label="Configuration"];
ConfGeneric [label="Generic", URL="#Generic_configuration"];
ConfTechnical [label="Technical", URL="#Technical_configuration"];

Configuration -> ConfGeneric;
Configuration -> ConfTechnical;

Regions [label="Regions", shape=tab, URL="#Generic_configuration"];
Locations [label="Locations", shape=tab, URL="#Generic_configuration"];
Units [label="Units", shape=tab, URL="#Generic_configuration"];
HealthFacilities [label="Health, Facilities" shape=tab, URL="#Generic_configuration"];
Physicians [label="Physicians", shape=tab, URL="#Generic_configuration"];
Gender [label="Gender", shape=tab, URL="#Generic_configuration"];
IdentificationCards [label="Identification Cards", shape=tab, URL="#Generic_configuration"];
StateOfTheRequest [label="State of the Request", shape=tab URL="#State_of_the_request"];

ConfGeneric -> Regions;
ConfGeneric -> Locations;
ConfGeneric -> Units;
ConfGeneric -> HealthFacilities;
ConfGeneric -> Physicians;
ConfGeneric -> Gender;
ConfGeneric -> IdentificationCards;
ConfGeneric -> StateOfTheRequest;

LaboratoryAreas [label="Laboratory Areas", shape=tab, URL="#Technical_configuration"];
AnalyticalTests [label="Analytical Tests", shape=tab URL="#Analytical_tests"];
AnalyticalTestsGroups [label="Analytical Tests Groups", shape=tab URL="#Analytical_tests_groups"];
AnalyticalProfiles [label="Analytical Profiles", shape=tab URL="#Analytical_profiles"];
KindsOfSamples [label="Kinds of Samples", shape=tab, URL="#Technical_configuration"];
SampleIncidents [label="Sample Incidents", shape=tab, URL="#Technical_configuration"];
SampleOrigins [label="Sample Origins", shape=tab, URL="#Technical_configuration"];
PregnancyPhases [label="Pregnancy Phases", shape=tab, URL="#Technical_configuration"];
DataTypes [label="Datatypes", shape=tab, URL="#Datatypes"];
ReportingOrder [label="Reporting Order", shape=tab, URL="#Reporting_order"];

ConfTechnical -> LaboratoryAreas;
ConfTechnical -> AnalyticalTests;
ConfTechnical -> AnalyticalTestsGroups;
ConfTechnical -> AnalyticalProfiles;
ConfTechnical -> KindsOfSamples;
ConfTechnical -> SampleIncidents;
ConfTechnical -> SampleOrigins;
ConfTechnical -> PregnancyPhases;
ConfTechnical -> DataTypes;
ConfTechnical -> ReportingOrder;

{ rank=same; Regions Units Physicians IdentificationCards LaboratoryAreas AnalyticalTestsGroups KindsOfSamples SampleOrigins DataTypes}
{ rank=same; ConfGeneric ConfTechnical}
{ rank=sink; Locations HealthFacilities Gender StateOfTheRequest AnalyticalTests AnalyticalProfiles SampleIncidents PregnancyPhases ReportingOrder}}
</graphviz>
</div>

__TOC__

The configuration functionality allows the user to manipulate ARIS, adding or changing some of its aspects for a better customization.
These have been divided into two groups, depending on the knowledge needed to use them.
The first group is absolutely generic and any person in the lab should be able to provide the required information.
However, for the second group, more specific biomedical knowledge will be needed.

==Generic configuration==
[[File:Genericconfiguration.PNG|right|600px|thumb|Editing the labels used for the states]]
This form controls the values of all non-free text fields (i.e., those that appear when clicking on an [[ARIS:User Guide#Arrow|arrow]]) within the system. Through each tab, the user is able to create, edit and delete the values of one of these fields.
If the laboratory is not interested in one of the values, but the user does not wish to delete the information from the system, it can be simply disabled, so it will not be shown in the corresponding drop-down menu. This is done by unticking the ''Active'' checkbox. </br> [[File:Activecheckbox.PNG|75px|Activated checkbox]] ⇔ [[File:Deactivatedcheckbox.PNG|75px|Deactivated checkbox]] </br>
List of tabs:
*Regions (initially empty)
*Locations (initially empty)
*Units
*Health Facilities (initially empty)
*Physicians (initially empty)
*Gender
*Identification cards
*State of the request

Some of them also include hierarchical information. Thus, physicians point to health facilities, health facilities point to locations and these to regions. This information is used in the forms to show the right available values depending on the parent choice in the hierarchy.

===State of the request===
From the ''state of the request'' tab, only the ''label'' field can be edited. Notice that this indicates the different phases a request goes through in the application during its lifecycle, and not only a passive value to be stored.

==Technical configuration==
The ''Laboratory areas'', ''Kinds of sample'', ''Sample incidents'', ''Sample origins'' and ''Pregnancy phases'' tabs, have exactly the same effect as the ones under the [[#Generic configuration|generic configuration]] (i.e., they simply provide the available values in drop boxes).
However, the following tabs have further effects in the behaviour of the forms.

===Analytical tests===
[[File:Analyticalprofile.PNG|right|thumb|700px| Editing analytical profiles]]
This is without doubt the most crucial concept in the configuration, since it defines the available kinds of tests in the laboratory.
They are identified by a name, but also contain a code that will always be shown next to the name.
To facilitate the management of the laboratory, kinds of tests are assigned to a laboratory area, which will be used both in the generation of reports for the patients, as well as in the analysis of data regarding the performance of the laboratory itself.

Each kind of test is then related to a kind of sample.
Only after that kind of sample is provided by the patient, the corresponding test will be allowed to have an associated result.

Each test must have a [[#Datatypes|datatype]], which indicates the kind of result it will accept, this being either numerical (integer or real) or enumerate.
For numerical test results, units of the test can be indicated for informative purposes, together with upper and lower bounds of the result can be defined.
These will be automatically checked.
Only results within the declared boundaries will get a green tick next to them.
Those outside the boundaries will be detected and automatically marked with a red cross.
Validating the value will rely anyway on the laboratory supervisor.
However, a note can be provided here to indicate exceptions to the boundaries or any information that is considered relevant to either the technician or the supervisor.

Finally, there are two specific boolean fields:
* Referred → Indicates that an action or test is performed in another hospital. The option marked in the configuration only determines the default of this field for each test. It does not impede the user from choosing differently in the [[ARIS:Requests|Requests]] forms.
* Automatic → Enables the kind of test to be partially automated. The result of the test is not manually obtained by a person, but by an AI. If this option is disabled in the configuration, the user will not be able to mark it otherwise in the [[ARIS:Requests|Requests]] forms. However, if it is enabled, the user will be able to choose if she desires for the test to be done automatically or not in the [[ARIS:Requests|Requests]] forms.

===Analytical tests groups===
In this tab, groups of tests can be formed for a quicker selection when choosing which tests to perform on a patient. When creating or editing a new group, a ''Group Of Tests Information'' form must be filled in or modified. In this form, the group must be given a name and the user must choose the tests included in the group from the box provided. In the left-hand side list, the groups are in alphabetical order and if the user wishes for a quicker option, there is a search bar on top of the box to write down and filter the tests.
Simply clicking on the name of a test adds it to the group, hence appearing in the right-hand side list.

The analytical tests groups are also used to sort the tests in the generated report of a request.

===Analytical profiles===
In this tab, profiles of tests can be formed for a quicker selection when choosing which groups of tests or individual tests to perform on a patient.
When creating or editing a new profile, an ''Analytical Profile Information'' form must be filled in or modified.
In this form, the profile must be given a name and the user must choose the tests and the groups included in the profile from the lists provided.
The groups and tests are in alphabetical order and if the user wishes for a quicker option, there is a search bar on top of the box to write down and filter the tests and groups.

Choosing a group selects in the corresponding list all the tests belonging to it.
Then, these cannot be individually removed from the profile, but only by removing the group.
Moreover, a test added later to the group will automatically appear as part of any profile containing that group, which is indicated by a lock icon next to the test name.

Analytical profiles do not have any effect in the report generated for a request.

===Datatypes===

Enumerate datatypes can be defined here (integer and real numbers are always available).
These are simply lists of potential results that can be used in any kind of test.

===Reporting order===
[[File:Reportingorder.PNG|Centre|500px|thumb|Editing the laboratory areas order from the reporting areas tab]]
This tab allows ordering the elements in the PDF worklist and in the report of a request.
The tests appearing in them will be firstly sorted by laboratory area, then groups of tests, and finally individual tests.
This is done by choosing one of the three elements, which will lead to another form with a list and two vertical arrows on the left side of the image.
Any number of elements can be simultaneously selected by simply clicking on them.
Then, the arrows will allow to move them up or down in the list, and hence in the generated PDF documents.