Posted on Sep 1, 2018

The Quick Analysis Wizard is designed to guide you through the process of easily and quickly uploading your images into a new experiment for automated processing. Once you get to the end of the wizard and click the 'Analyze' button, your analysis jobs will start and you will receive email links as the jobs make progress through the final report generation.

At each step we have provided how-to demonstration videos that give you step by step instructions.

At any point if your question is not answered, please send an email to support@metavilabs.com.

1. Description Field

The description you provide will be the key to finding your experiment results later. It's important to make it as unique as possible. You can put as much information into the description as you wish. If you use the advanced mode of experiment creation, you can also add your experimental parameters in their own fields. This keeps all your experiment data organized in a database that is easily searchable and accessible from any computer.

2. Image Resolution

The image resolution is a very important input to get correct. All results are calculated in microns or micron². The algorithms use this resolution factor to convert pixel values into distances. This is also how the algorithms do an excellent job finding cells structures - by knowing what the distance scales to optimize cell detection. Please read this tech-note on calculating pixel resolution.

3. Choosing Your Assay

Each customer account receives 15 processing jobs per month.  A processing job is defined as the processing of a well containing an image or set of time-lapse images.  A single glass slide would typically be considered one well.

You can purchase processing jobs at any time using the Account link in the navigation menu followed clicking on the "Jobs Requests" tab.

You can read about each assay in the Assay Guide.

The Quick Analysis Wizard is designed to guide you through the process of easily and quickly uploading your images into a new experiment for automated processing. Once you get to the end of the wizard and click the 'Analyze' button, your analysis jobs will start and you will receive email links as the jobs make progress through the final report generation.

At each step we have provided how-to demonstration videos that give you step by step instructions.

At any point if your question is not answered, please send an email to support@metavilabs.com.

1. Description Field

The description you provide will be the key to finding your experiment results later. It's important to make it as unique as possible. You can put as much information into the description as you wish. If you use the advanced mode of experiment creation, you can also add your experimental parameters in their own fields. This keeps all your experiment data organized in a database that is easily searchable and accessible from any computer.

2. Image Resolution

The image resolution is a very important input to get correct. All results are calculated in microns or micron². The algorithms use this resolution factor to convert pixel values into distances. This is also how the algorithms do an excellent job finding cells structures - by knowing what the distance scales to optimize cell detection. Please read this tech-note on calculating pixel resolution.

3. Choosing Your Assay

Each customer account receives 15 processing jobs per month.  A processing job is defined as the processing of a well containing an image or set of time-lapse images.  A single glass slide would typically be considered one well.

You can purchase processing jobs at any time using the Account link in the navigation menu followed clicking on the "Jobs Requests" tab.

You can read about each assay in the Assay Guide.

Posted on Sep 1, 2018

upload 96 wells of microscopy images

Quick Analysis Wizard

ACAS is designed to allow you to easily upload up to 96 wells of data with a few mouse clicks. There are many ways your data can be organized on your computer disk. The Quick Analysis Wizard is designed to help ACAS determine how your files are organized.

This page will get you started on the Quick Analysis Wizard (the easiest way to get started). If you prefer not to use the wizard, try our Advanced Guide to Working with Projects (and advanced multi-well upload).

Select one:

upload 96 wells of microscopy images

Quick Analysis Wizard

ACAS is designed to allow you to easily upload up to 96 wells of data with a few mouse clicks. There are many ways your data can be organized on your computer disk. The Quick Analysis Wizard is designed to help ACAS determine how your files are organized.

This page will get you started on the Quick Analysis Wizard (the easiest way to get started). If you prefer not to use the wizard, try our Advanced Guide to Working with Projects (and advanced multi-well upload).

Select one:

Posted on Sep 1, 2018

Before undertaking a custom project, we need to collect some basic information to make sure we can get the job done right the first time.

  1. Are the cells on a 2D surface or in a 3D matrix?
    1. if 3D, are z-stacks created?
    2. Is tracking between z-stacks required?
  2. What is the maximum and typical diameter of the cells?
  3. What is the imaging technique?
    1. bright-field (not recommended)
    2. dark-field (preferred)
    3. phase-contrast (preferred)
    4. fluorescence
      1. how many channels
      2. list the color labels and what each label represents
  4. What is the camera resolution (in pixels) and the field of view width (in micrometers)?
  5. What type of chambers are being used?
    1. ibidi µ-Slide
    2. Dunn chamber
    3. Other?
  6. What is being measured?
  7. Are there specific csv file data formats required for the results?
  8. What is the file format of the images?
    1. Time-lapse or endpoint?
    2. If time-lapse, are the source files
      1. mp4, avi, or mov files?
      2. a folder with a collection of bmp, jpg, png, or tif, that makes up one movie?
      3. multi-frame tif files with one time-lapse per tif?
      4. a folder containing tif files, where each tif file contains multiple fluorescence channels, and multiple tiff files make up one time-lapse sequence?

 

 

Before undertaking a custom project, we need to collect some basic information to make sure we can get the job done right the first time.

  1. Are the cells on a 2D surface or in a 3D matrix?
    1. if 3D, are z-stacks created?
    2. Is tracking between z-stacks required?
  2. What is the maximum and typical diameter of the cells?
  3. What is the imaging technique?
    1. bright-field (not recommended)
    2. dark-field (preferred)
    3. phase-contrast (preferred)
    4. fluorescence
      1. how many channels
      2. list the color labels and what each label represents
  4. What is the camera resolution (in pixels) and the field of view width (in micrometers)?
  5. What type of chambers are being used?
    1. ibidi µ-Slide
    2. Dunn chamber
    3. Other?
  6. What is being measured?
  7. Are there specific csv file data formats required for the results?
  8. What is the file format of the images?
    1. Time-lapse or endpoint?
    2. If time-lapse, are the source files
      1. mp4, avi, or mov files?
      2. a folder with a collection of bmp, jpg, png, or tif, that makes up one movie?
      3. multi-frame tif files with one time-lapse per tif?
      4. a folder containing tif files, where each tif file contains multiple fluorescence channels, and multiple tiff files make up one time-lapse sequence?

 

 

Posted on Sep 1, 2018

Please watch the how-to video above for help on signup. If you have any problems you can contact us at support@metavilabs.com.

Please watch the how-to video above for help on signup. If you have any problems you can contact us at support@metavilabs.com.

Posted on Sep 1, 2018

NOTE:  Internet Explorer 10 and 11 do not support multi-folder upload.  We recommend Chrome and Firefox for the best experience uploading many wells.

Getting Started with ACAS

This page will help you get started with ACAS as quickly as possible. Our goal is to make you much more productive with automation.

We are passionate that our solution does exactly what you need it to do to make your job easier. If at any point the software does not do exactly what you need, we view this is an opportunity to make an improvement.

Please let us know how we can add features to our analysis, reports, and documentation !

If you can't find what you need, please email us at support@metavilabs.com

Suggested First Steps

It should take about 10 minutes to get through the following reading. After your initial experiment, uploading a new experiment in ACAS takes about 60 seconds. Your experiment results will typically be available on-line about ten minutes later.

  1. Find the Try it Yourself and Sample Movies sections in the Assay guide for your specific assay.  Assay Guides here.
  2. Read the Calculating Pixel Resolution Guide.
  3. Follow the steps in Get Started by Running A Quick Analysis .  Following the quiz links will get you to the how-to-video that will be most appropriate for your situation.

Getting Help

  1. Look for the Help icon on select pages to get context sensitive help on a topic. metavi labs help icon
  2.  Browse the Documentation.

https://www.metavilabs.com/documentation

3. Go to the Help Center from any page by clicking the Help Center Icon that is on your navigation menu. metavi labs help center menu link

Setting Up your account

You will access your account with a custom URL (address that is used in your web browser).  The best practice is to use the name of your university/company plus additional text that uniquely identifies your group within your organization.  Please record this URL and bookmark it in your browser.

Watch this how-to video to learn how to set up your account.

https://www.metavilabs.com/researcher-signup

Get Started by running a Quick Analysis

Using your 15 free jobs per month (you can purchase more any time), give the system a try. The following video takes just a couple of minutes and will give you the information you need to create your first experiment in ACAS.

https://www.metavilabs.com/quick-analysis-wizard-easily-get-your-files-uploaded-acas

In the following link you will find your assay guide to get the details for the assay you will be using.

https://www.metavilabs.com/setting-assay-options

How to Purchase Analysis Jobs

https://www.metavilabs.com/help-purchasing-analysis-jobs

ACAS Help Center

The following link take you to the ACAS help center where you will find all the supporting documentation.

https://www.metavilabs.com/documentation

If at any point our documentation leaves you with open questions, please don't hesitate to send us an email. Also, if our software does not provide the data you need, or the algorithm does not appear to be working as expected, we are happy to make changes. Many tweaks to the software can be done in one to two weeks.

Our contact email: support@metavilabs.com

NOTE:  Internet Explorer 10 and 11 do not support multi-folder upload.  We recommend Chrome and Firefox for the best experience uploading many wells.

Getting Started with ACAS

This page will help you get started with ACAS as quickly as possible. Our goal is to make you much more productive with automation.

We are passionate that our solution does exactly what you need it to do to make your job easier. If at any point the software does not do exactly what you need, we view this is an opportunity to make an improvement.

Please let us know how we can add features to our analysis, reports, and documentation !

If you can't find what you need, please email us at support@metavilabs.com

Suggested First Steps

It should take about 10 minutes to get through the following reading. After your initial experiment, uploading a new experiment in ACAS takes about 60 seconds. Your experiment results will typically be available on-line about ten minutes later.

  1. Find the Try it Yourself and Sample Movies sections in the Assay guide for your specific assay.  Assay Guides here.
  2. Read the Calculating Pixel Resolution Guide.
  3. Follow the steps in Get Started by Running A Quick Analysis .  Following the quiz links will get you to the how-to-video that will be most appropriate for your situation.

Getting Help

  1. Look for the Help icon on select pages to get context sensitive help on a topic. metavi labs help icon
  2.  Browse the Documentation.

https://www.metavilabs.com/documentation

3. Go to the Help Center from any page by clicking the Help Center Icon that is on your navigation menu. metavi labs help center menu link

Setting Up your account

You will access your account with a custom URL (address that is used in your web browser).  The best practice is to use the name of your university/company plus additional text that uniquely identifies your group within your organization.  Please record this URL and bookmark it in your browser.

Watch this how-to video to learn how to set up your account.

https://www.metavilabs.com/researcher-signup

Get Started by running a Quick Analysis

Using your 15 free jobs per month (you can purchase more any time), give the system a try. The following video takes just a couple of minutes and will give you the information you need to create your first experiment in ACAS.

https://www.metavilabs.com/quick-analysis-wizard-easily-get-your-files-uploaded-acas

In the following link you will find your assay guide to get the details for the assay you will be using.

https://www.metavilabs.com/setting-assay-options

How to Purchase Analysis Jobs

https://www.metavilabs.com/help-purchasing-analysis-jobs

ACAS Help Center

The following link take you to the ACAS help center where you will find all the supporting documentation.

https://www.metavilabs.com/documentation

If at any point our documentation leaves you with open questions, please don't hesitate to send us an email. Also, if our software does not provide the data you need, or the algorithm does not appear to be working as expected, we are happy to make changes. Many tweaks to the software can be done in one to two weeks.

Our contact email: support@metavilabs.com

Posted on Aug 8, 2018

Cytotoxic T cells are those cells of the immune system that are naturally destined to kill cells of the body that display an aberrant expression of antigens such as virus-infected cells and tumor cells. Their duty is based on two functions: find the pathogenic cell and kill it. Novel immune therapy approaches have armed cytotoxic T cells with special receptors, the so-called chimeric antigen receptors (CAR), that enables these cytotoxic T cells to efficiently kill their target, especially with regard to cancer cells. Several clinical studies on various types of cancer are currently ongoing.

Quantification of killing, the decision between life and death is easy to measure in a lab in order to verify the functionality of the CAR T cells. In contrast, movement of these cells towards a pathogenic cell – a process that we have termed as Pathotaxis – is a gradual cell function that is very difficult to quantify. But if the CAR T cells don’t find their target, they cannot kill it. This vitally essential issue of inappropriate trafficking is addressed in this paper. MetaVi Labs is providing solutions to overcome these hurdles in pre-clinical research of CAR T cell immunotherapy and any other cell-based therapeutic approaches.

Read the paper at Pubmed: "Chimeric Antigen Receptors T Cell Therapy in Solid Tumor: Challenges and Clinical Applications"

Posted on Jul 14, 2018

A 2D imaging experiment setup is preferred for un-labeled cell tracking of smaller cells such as immune cells. In MetaVi Labs' pathotaxis experiments when immune cells are co-cultured with pathogenic cells, 2D allows improved tracking of the immune cells (when the immune cells are un-labeled).

While tumor cells will adhere to glass or plastic, immune cells require a protein coating. Fortunately, this is easily accomplished with slides from ibidi.

Modifications to ibidi Protocols

We recommend ibidi slides and their associated protocols. However, please note:

  1. The ibidi recommendations for cell density are not applicable to many Pathotaxis experiments. We recommend finding the minimum cell densities possible to allow for greater accuracy in tracking and analysis, while still accomplishing the biological aim.
  2. For T-cell experiments, we recommend imaging at least one image per 30 seconds (or faster) if it is desired to track T-cell movement.
  3. In 2D experiments, cell adhesion should begin within 30 minutes of application of the cell media to the slide. Imaging should start at the 30-minute mark.

µ-Slide Chemotaxis

Used to investigate chemotaxis of fast or slow migrating adherent cells and non-adherent cells in gel matrices.

T-Cell Adhesion

This chamber can be used for non-traditional-chemotaxis experiments (i.e., experiments in which cell migration is important but an external chemo-attractant is not being used but rather the T-cells will be demonstrating Pathotaxis due to the pathogenic cells). This chamber has the advantage of a surface coating to which T-Cells will adhere. The product has two surface coating options, ibid-Treat, and Collagen IV. Other labs have had successful T-Cell adhesion with the Collagen IV surface coating.

Ordering Information

Catalog Number 80322

Surface Modification: Collagen IV: #1.5 polymer coverslip, sterilized.

Protocol

The ibidi Application Note 17 has a detailed protocol for 2D experiments.

Application Note 17: 2D and 3D Chemotaxis Assays Using µ-Slide Chemotaxis

µ-Slide 8-Well

An open µ-Slide (chambered coverslip) with 8 wells for use in immunofluorescence and high-end microscopy.

T-Cell Adhesion

This chamber has the advantage of a variety of surface coatings. Other labs have had successful T-Cell adhesion with the Collagen IV surface coating.

Ordering Information

Catalog Number 80822

Surface Modification: Collagen IV: #1.5 polymer coverslip, sterilized.

Protocol

The following link provides the detailed usage instructions for this versatile plate:

µ-Slide 8 Well Detailed Protocol

Custom Surface Coatings

The ibidi slides can also be ordered with either no-coating or the ibidi-Treat coating. This allows for creating your own coating.

Coating procedures for ibidi µ-Slides and µ-Dishes

For optimized cell adhesion, there are different treatments and coatings for the ibidi labware family. The ibiTreat surface is comparable to standard tissue culture treated labware. This surface permits direct cell growth with a large number of cell lines and primary cells. Compared to the ibiTreat surface, the uncoated surface is very hydrophobic. The uncoated surface must be coated with a protein solution for the adhesion of most cells.

Recommended Surfaces

  • For Collagen I: ibiTreat (tissue culture treated)
  • For Collagen IV: ibiTreat (tissue culture treated) or hydrophobic, uncoated
  • For Fibronectin: ibiTreat (tissue culture treated) or hydrophobic, uncoated
  • For Poly-L-Lysine: ibiTreat (tissue culture treated)
  • For Poly-D-Lysine: ibiTreat (tissue culture treated)

To establish a specific coating relevant to a specific research application, we recommend testing the coating procedure on both uncoated and ibiTreat µ-Slides. We have observed that some biomolecules adhere differently to hydrophobic and hydrophilic plastic surfaces. Please note that there is no uncoated version of the µ-Slide Chemotaxis. Use the ibiTreat surface for all coatings. Some products are also offered with a glass bottom. Glass can also be coated according to the specifications below. The ESS surface needs higher protein concentrations for an effective coating and must not be dried after coating.

Complete Application Note for Custom Surfaces

Reference Paper for T-cell Migration on 2D Surface

This open access paper describes T-cell migration mechanisms and utilized the ibidi µ-Slide Chemotaxis with Collagen IV surface treatment.

T Lymphocyte Migration: An Action Movie Starring the Actin and Associated Actors

A 2D imaging experiment setup is preferred for un-labeled cell tracking of smaller cells such as immune cells. In MetaVi Labs' pathotaxis experiments when immune cells are co-cultured with pathogenic cells, 2D allows improved tracking of the immune cells (when the immune cells are un-labeled).

While tumor cells will adhere to glass or plastic, immune cells require a protein coating. Fortunately, this is easily accomplished with slides from ibidi.

Modifications to ibidi Protocols

We recommend ibidi slides and their associated protocols. However, please note:

  1. The ibidi recommendations for cell density are not applicable to many Pathotaxis experiments. We recommend finding the minimum cell densities possible to allow for greater accuracy in tracking and analysis, while still accomplishing the biological aim.
  2. For T-cell experiments, we recommend imaging at least one image per 30 seconds (or faster) if it is desired to track T-cell movement.
  3. In 2D experiments, cell adhesion should begin within 30 minutes of application of the cell media to the slide. Imaging should start at the 30-minute mark.

µ-Slide Chemotaxis

Used to investigate chemotaxis of fast or slow migrating adherent cells and non-adherent cells in gel matrices.

T-Cell Adhesion

This chamber can be used for non-traditional-chemotaxis experiments (i.e., experiments in which cell migration is important but an external chemo-attractant is not being used but rather the T-cells will be demonstrating Pathotaxis due to the pathogenic cells). This chamber has the advantage of a surface coating to which T-Cells will adhere. The product has two surface coating options, ibid-Treat, and Collagen IV. Other labs have had successful T-Cell adhesion with the Collagen IV surface coating.

Ordering Information

Catalog Number 80322

Surface Modification: Collagen IV: #1.5 polymer coverslip, sterilized.

Protocol

The ibidi Application Note 17 has a detailed protocol for 2D experiments.

Application Note 17: 2D and 3D Chemotaxis Assays Using µ-Slide Chemotaxis

µ-Slide 8-Well

An open µ-Slide (chambered coverslip) with 8 wells for use in immunofluorescence and high-end microscopy.

T-Cell Adhesion

This chamber has the advantage of a variety of surface coatings. Other labs have had successful T-Cell adhesion with the Collagen IV surface coating.

Ordering Information

Catalog Number 80822

Surface Modification: Collagen IV: #1.5 polymer coverslip, sterilized.

Protocol

The following link provides the detailed usage instructions for this versatile plate:

µ-Slide 8 Well Detailed Protocol

Custom Surface Coatings

The ibidi slides can also be ordered with either no-coating or the ibidi-Treat coating. This allows for creating your own coating.

Coating procedures for ibidi µ-Slides and µ-Dishes

For optimized cell adhesion, there are different treatments and coatings for the ibidi labware family. The ibiTreat surface is comparable to standard tissue culture treated labware. This surface permits direct cell growth with a large number of cell lines and primary cells. Compared to the ibiTreat surface, the uncoated surface is very hydrophobic. The uncoated surface must be coated with a protein solution for the adhesion of most cells.

Recommended Surfaces

  • For Collagen I: ibiTreat (tissue culture treated)
  • For Collagen IV: ibiTreat (tissue culture treated) or hydrophobic, uncoated
  • For Fibronectin: ibiTreat (tissue culture treated) or hydrophobic, uncoated
  • For Poly-L-Lysine: ibiTreat (tissue culture treated)
  • For Poly-D-Lysine: ibiTreat (tissue culture treated)

To establish a specific coating relevant to a specific research application, we recommend testing the coating procedure on both uncoated and ibiTreat µ-Slides. We have observed that some biomolecules adhere differently to hydrophobic and hydrophilic plastic surfaces. Please note that there is no uncoated version of the µ-Slide Chemotaxis. Use the ibiTreat surface for all coatings. Some products are also offered with a glass bottom. Glass can also be coated according to the specifications below. The ESS surface needs higher protein concentrations for an effective coating and must not be dried after coating.

Complete Application Note for Custom Surfaces

Reference Paper for T-cell Migration on 2D Surface

This open access paper describes T-cell migration mechanisms and utilized the ibidi µ-Slide Chemotaxis with Collagen IV surface treatment.

T Lymphocyte Migration: An Action Movie Starring the Actin and Associated Actors