Posted on Sep 3, 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.

In this example, the parent folder is selected and dropped into the drop-box. But you can also drag individual files or folders. Its best to select and drag the first parent folder that contains all the files you want to upload.

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

In this example, the parent folder is selected and dropped into the drop-box. But you can also drag individual files or folders. Its best to select and drag the first parent folder that contains all the files you want to upload.

Posted on Sep 3, 2018

All ACAS experiment-sets require the user to enter the pixel per µm resolution of the uploaded images (i.e. the number of pixels for each µm of distance in the image).

This is a critical measurement and is used in two ways:

a) the ACAS software reads the number of pixels in the image, but it cannot know how many pixels a typical cell will occupy without this distance factor. This allows the algorithms to optimize the detection of structures.

b) the ACAS software reports its findings in terms of µm lengths and areas. Without this factor, it would report in pixels and leave the final conversions to µm to the researcher.

Resolutions lower than 0.4 pix/µm typically do not provide enough visual information for successful analysis. The typical range we see is 0.5 to 2.0 pix/µm.

Advanced Guide to Pixel Resolution

Advanced Guide to Pixel Resolution, provided by ibidi

Please note the ibidi technical note uses µm/pix whereas ACAS uses pix/µm.

So to get the units required by ACAS, simply  invert the result ( 1 divided by ibidi-number).

The Simple Calculation

The (pixel / µm) resolution is calculated by :

microscopy image resolution formula 1

A common mistake is to invert the calculation. If your microscope software provides resolution in µm/pixel, then you can simply apply 1/x to get the resolution in pixels/µm.

Your microscope imaging software should provide the image width in pixels as well as the image width in microns. If not, refer to the advanced guide linked at the bottom.

As an example, the following image has a resolution of 1.24, which is given by: 2048 pixels divided by 1648 um.

microscopy sample image

Automated Resolution Detection

The ACAS software analyzes the image to detect round-cells in an effort to estimate the image resolution.

However, the ACAS automated resolution detection is not accurate and only used to detect gross errors in the input (for example, the objective zoom may not have been considered in the calculation, or the units were inverted).

If the provided resolution is significantly different from the detected resolution, the user will see a warning in the final report in the Settings Tab and will be asked to validate the provided resolution. If the user is confident in the resolution, the warning can be ignored.

All ACAS experiment-sets require the user to enter the pixel per µm resolution of the uploaded images (i.e. the number of pixels for each µm of distance in the image).

This is a critical measurement and is used in two ways:

a) the ACAS software reads the number of pixels in the image, but it cannot know how many pixels a typical cell will occupy without this distance factor. This allows the algorithms to optimize the detection of structures.

b) the ACAS software reports its findings in terms of µm lengths and areas. Without this factor, it would report in pixels and leave the final conversions to µm to the researcher.

Resolutions lower than 0.4 pix/µm typically do not provide enough visual information for successful analysis. The typical range we see is 0.5 to 2.0 pix/µm.

Advanced Guide to Pixel Resolution

Advanced Guide to Pixel Resolution, provided by ibidi

Please note the ibidi technical note uses µm/pix whereas ACAS uses pix/µm.

So to get the units required by ACAS, simply  invert the result ( 1 divided by ibidi-number).

The Simple Calculation

The (pixel / µm) resolution is calculated by :

microscopy image resolution formula 1

A common mistake is to invert the calculation. If your microscope software provides resolution in µm/pixel, then you can simply apply 1/x to get the resolution in pixels/µm.

Your microscope imaging software should provide the image width in pixels as well as the image width in microns. If not, refer to the advanced guide linked at the bottom.

As an example, the following image has a resolution of 1.24, which is given by: 2048 pixels divided by 1648 um.

microscopy sample image

Automated Resolution Detection

The ACAS software analyzes the image to detect round-cells in an effort to estimate the image resolution.

However, the ACAS automated resolution detection is not accurate and only used to detect gross errors in the input (for example, the objective zoom may not have been considered in the calculation, or the units were inverted).

If the provided resolution is significantly different from the detected resolution, the user will see a warning in the final report in the Settings Tab and will be asked to validate the provided resolution. If the user is confident in the resolution, the warning can be ignored.

Posted on Sep 3, 2018

ImagesToMovie is a free program MetaVi Labs offers its customers to easily convert a set of raw images into compressed movie files that are easily up loadable to our ACAS software.

Demonstration Video

Link to Installer

This is a Microsoft Windows only program. When you click on the link below, your browser should give you the chance to download this and run it. It will install it in your programs folder under MetaVi Labs/ImagesToMovie

Depending on your browser, you may have to right-click over the link and choose “save link as…” to download it.

Link to setup executable.


How To Un-Install a Previous Version (Windows 10)

Remove in Settings

1. Select the Start button, then select Settings > Apps.
2. Choose the program you want to remove, and then select Uninstall. Some apps built into Windows can’t be uninstalled.

ImagesToMovie is a free program MetaVi Labs offers its customers to easily convert a set of raw images into compressed movie files that are easily up loadable to our ACAS software.

Demonstration Video

Link to Installer

This is a Microsoft Windows only program. When you click on the link below, your browser should give you the chance to download this and run it. It will install it in your programs folder under MetaVi Labs/ImagesToMovie

Depending on your browser, you may have to right-click over the link and choose “save link as…” to download it.

Link to setup executable.


How To Un-Install a Previous Version (Windows 10)

Remove in Settings

1. Select the Start button, then select Settings > Apps.
2. Choose the program you want to remove, and then select Uninstall. Some apps built into Windows can’t be uninstalled.

Posted on Sep 3, 2018

If you are uploading multi-frame files (mp4, avi, mov, tif), the file size is limited to 150 MB.

If you are uploading single frame images (jpg, bmp, png) the file size limit is 150 MB for the aggregate of all the images.  When uploading 30 images or less, the ACAS system  will aggregate all your uploaded files into a single zip file per well. When uploading more than 30 images, the files will be aggregated into an mp4 movie file. The movie file compression may result in a aggregated file size which is smaller than the total of the individual frames.

The free Individual Researcher account is limited to 5 GB of storage. To save storage space and decrease upload times, we recommend that single frames should be stored as jpg or png files rather than bmp (bmp files are not compressed).

For time-lapse movies, we recommend h.264 compression inside an mp4 container.

If you are uploading multi-frame files (mp4, avi, mov, tif), the file size is limited to 150 MB.

If you are uploading single frame images (jpg, bmp, png) the file size limit is 150 MB for the aggregate of all the images.  When uploading 30 images or less, the ACAS system  will aggregate all your uploaded files into a single zip file per well. When uploading more than 30 images, the files will be aggregated into an mp4 movie file. The movie file compression may result in a aggregated file size which is smaller than the total of the individual frames.

The free Individual Researcher account is limited to 5 GB of storage. To save storage space and decrease upload times, we recommend that single frames should be stored as jpg or png files rather than bmp (bmp files are not compressed).

For time-lapse movies, we recommend h.264 compression inside an mp4 container.

Posted on Sep 3, 2018

This page will help determine how to handle your time-lapse files. Please read below the two options and at the bottom of this page click on the link that best describes your situation.

Single Folder

All movie files are contained in one folder. Each file is a movie from a well. So if you have 96 wells, you have 96 movie files in one folder. The file names will become the well names in ACAS.

By Folder

Your files are organized with one folder for each well. Each folder contains one movie file or a time-lapse series of still frames. The folder name will be the well name in ACAS.

Allowed File Formats:


Allowed time-lapse file formats:

mp4 (preferred), avi, mov, multi-frame-tif, zip

If organized by folder, each folder can contain a time series of:

png (preferred), jpg, bmp, tif

So we can show you the correct demo video for your situation, please click on one of the blue arrows below:

This page will help determine how to handle your time-lapse files. Please read below the two options and at the bottom of this page click on the link that best describes your situation.

Single Folder

All movie files are contained in one folder. Each file is a movie from a well. So if you have 96 wells, you have 96 movie files in one folder. The file names will become the well names in ACAS.

By Folder

Your files are organized with one folder for each well. Each folder contains one movie file or a time-lapse series of still frames. The folder name will be the well name in ACAS.

Allowed File Formats:


Allowed time-lapse file formats:

mp4 (preferred), avi, mov, multi-frame-tif, zip

If organized by folder, each folder can contain a time series of:

png (preferred), jpg, bmp, tif

So we can show you the correct demo video for your situation, please click on one of the blue arrows below:

Posted on Sep 3, 2018

Providing the 'time lapse'/'single frame' selection helps ACAS upload your files correctly.  In the next step you will be asked about your file layout on your disk drive.  This facilitates the drag and drop feature.

Later when reports are generated, the report format will change depending on the number of frames found in each well. Any well that contains two or more files is treated as time lapse and the tracked values will be plotted over time. If only a single image file is found in a well, the reports will plot data as single values correlated between the wells.

An overview of the entire file upload process is found here:

Providing the 'time lapse'/'single frame' selection helps ACAS upload your files correctly.  In the next step you will be asked about your file layout on your disk drive.  This facilitates the drag and drop feature.

Later when reports are generated, the report format will change depending on the number of frames found in each well. Any well that contains two or more files is treated as time lapse and the tracked values will be plotted over time. If only a single image file is found in a well, the reports will plot data as single values correlated between the wells.

An overview of the entire file upload process is found here:

Posted on Sep 3, 2018

When making time-lapse movies in multiple fluorescent channels, how to format the data can be very confusing. Each microscope is different in what its software prefers to export.

The bottom line is we can work with pretty much anything except proprietary formats. But we have our preferences.

MetaVi Labs preference order is:

First Choice

Each channel is in a separate mp4 file (using H.264 compression internally). The images are gray-scale. Keeping the channels separate will provide more accuracy than pre-composited images. MetaVi Labs software will composite and colorize the images for display after the tracking.

Second Choice

Each channel is associated with one folder, and each folder has a collection of tiff files, one file per time point.

Third Choice

Each time point is contained in a multi-frame tiff file. Each file has one image from each of the channels. Each image is grey-scale.

When making time-lapse movies in multiple fluorescent channels, how to format the data can be very confusing. Each microscope is different in what its software prefers to export.

The bottom line is we can work with pretty much anything except proprietary formats. But we have our preferences.

MetaVi Labs preference order is:

First Choice

Each channel is in a separate mp4 file (using H.264 compression internally). The images are gray-scale. Keeping the channels separate will provide more accuracy than pre-composited images. MetaVi Labs software will composite and colorize the images for display after the tracking.

Second Choice

Each channel is associated with one folder, and each folder has a collection of tiff files, one file per time point.

Third Choice

Each time point is contained in a multi-frame tiff file. Each file has one image from each of the channels. Each image is grey-scale.