Posted on Sep 3, 2018

About Plate Selection and Reports

Because the final report will compare results from all wells in the plate, the plate selection is important for creating the correct number of wells. For example, if you choose a 24 well plate, 24 wells will be created and the report will compare the results for 24 wells.  The reports will not be automatically generated until all 24 wells have been populated with input images and those images have been processed.

If you only upload say 20 wells in a 24 well plate, you will not get a report. If you don't intent to upload all 24 wells, you can delete the remaining open wells, then click the report generation icon: report icon

Note: If you choose a plate with multiple wells but do not upload images for all of the wells, a report will not be generated. The report tool waits for results from all wells before generating a final report.

The Custom Plate

The Custom plate is the most flexible. The Custom plate is very flexible because the number of wells is determined when you upload your files. Any number starting from 1 is allowed.

Your well names will be assigned based on the name of the files uploaded or the folders containing the files. These well names will be propagated to your final report.

Manually Generating A Report

You can always edit the well names and regenerate a report by clicking on the report icon shown here: report icon

Well Naming

If you use the wizard to upload files, the wells will be renamed using the file name (or folder name if you have one folder per well).  But if you upload one image file for each well manually, then you will have the option to keep the default well name or use the file name.

Click here to view the plate guide:

selecting plates

About Plate Selection and Reports

Because the final report will compare results from all wells in the plate, the plate selection is important for creating the correct number of wells. For example, if you choose a 24 well plate, 24 wells will be created and the report will compare the results for 24 wells.  The reports will not be automatically generated until all 24 wells have been populated with input images and those images have been processed.

If you only upload say 20 wells in a 24 well plate, you will not get a report. If you don't intent to upload all 24 wells, you can delete the remaining open wells, then click the report generation icon: report icon

Note: If you choose a plate with multiple wells but do not upload images for all of the wells, a report will not be generated. The report tool waits for results from all wells before generating a final report.

The Custom Plate

The Custom plate is the most flexible. The Custom plate is very flexible because the number of wells is determined when you upload your files. Any number starting from 1 is allowed.

Your well names will be assigned based on the name of the files uploaded or the folders containing the files. These well names will be propagated to your final report.

Manually Generating A Report

You can always edit the well names and regenerate a report by clicking on the report icon shown here: report icon

Well Naming

If you use the wizard to upload files, the wells will be renamed using the file name (or folder name if you have one folder per well).  But if you upload one image file for each well manually, then you will have the option to keep the default well name or use the file name.

Click here to view the plate guide:

selecting plates

Posted on Sep 3, 2018

We find that two-channel fluorescence imaging with a zoom factor of 5X to 10X and a high-resolution camera produce the best results. To achieve optimal tracking we suggest you should attempt to duplicate the sample images below in terms of contrast and resolution.

Imaging Mode fluorescence on inverted microscope
Camera Resolution 2048 pixels wide or greater
Field-of-view approximately 1 mm x 1 mm
Microscopy Resolution optimal 3.0 pix/µm, minimum: 0.5 pix/µm (calculating microscopy resolution tech note)
Glass Slide See 'Recommended Chambers' section below.
Time-lapse Recording mp4 movie file containing H.264 encoded images
Time-between-frames One frame recorded each 30 seconds

Sample Fluorescence-Based Imaging

FIBROBLASTS IN 2D COLLAGEN

Imaging Mode Dark-field, inverted microscope
Camera Resolution 1280 x 1024
Field-of-view 1,200 µm to 1,612µm (cropped from original)
Microscopy Resolution 0.623 pix/µm
Glass Slide high-quality flat bottom glass ibidi µ-Dish 35 with high resolution glass bottom

darkfield fibroblast microscopy image

BREAST CANCER CELLS IN 3D COLLAGEN

Imaging Mode Dark-field, inverted microscope
Camera Resolution 2080 x 1584
Field-of-view approximately 1 mm x 1 mm
Microscopy Resolution 2.06 pix/µm
Glass Slide standard glass slide
darkfield breastcancer microscopy cells

Sample mp4/H.264 encoded movie from the microscopy setup described above:

We find that two-channel fluorescence imaging with a zoom factor of 5X to 10X and a high-resolution camera produce the best results. To achieve optimal tracking we suggest you should attempt to duplicate the sample images below in terms of contrast and resolution.

Imaging Mode fluorescence on inverted microscope
Camera Resolution 2048 pixels wide or greater
Field-of-view approximately 1 mm x 1 mm
Microscopy Resolution optimal 3.0 pix/µm, minimum: 0.5 pix/µm (calculating microscopy resolution tech note)
Glass Slide See 'Recommended Chambers' section below.
Time-lapse Recording mp4 movie file containing H.264 encoded images
Time-between-frames One frame recorded each 30 seconds

Sample Fluorescence-Based Imaging

FIBROBLASTS IN 2D COLLAGEN

Imaging Mode Dark-field, inverted microscope
Camera Resolution 1280 x 1024
Field-of-view 1,200 µm to 1,612µm (cropped from original)
Microscopy Resolution 0.623 pix/µm
Glass Slide high-quality flat bottom glass ibidi µ-Dish 35 with high resolution glass bottom

darkfield fibroblast microscopy image

BREAST CANCER CELLS IN 3D COLLAGEN

Imaging Mode Dark-field, inverted microscope
Camera Resolution 2080 x 1584
Field-of-view approximately 1 mm x 1 mm
Microscopy Resolution 2.06 pix/µm
Glass Slide standard glass slide
darkfield breastcancer microscopy cells

Sample mp4/H.264 encoded movie from the microscopy setup described above:

Posted on Sep 3, 2018

A well may contain a single image, or it may contain a time-lapse sequence.

Supported file types for single images are .bmp, .jpg, .png, .tif, .tiff.

For many experiments, the well will contain a time sequence of images.

Supported file types for time-lapse sequences are:

a) a collection of single images with the file types .bmp, .jpg, .png, .tif, .tiff. If you supply a collection of single images, be sure that the order of the images corresponds with the time order when the files are sorted alpha-numerically. On a Microsoft operating system, after sorting files by 'name', the files should be in time sequence where time zero is the first file.

b) a movie or multi-frame container such as .mp4, .tif, .tiff, .avi, .mov.

How to Upload a Collection of Frames

Generally, microscope recording systems will output a series of bitmaps or tif files. Tif files can contain a single image or a sequence of images.

upload images or moview

Any of these formats can be uploaded to the well. First determine if your image set is already contained in a single file (for example, mp4, avi, mov, or multi-frame tif). If so you can just directly upload these movie files to the well. Note, only one movie file per well.

If your image sequence is not contained in a movie file, you can also easily upload this sequence of images using the 'multi-image selection' button on the file uploader.

example multi-frame select

Now click "Choose Files". Click on the first file, then hold the shift key and click on the last file in the list, then all files will be selected.

Note: be sure the image file names are alphabetical in time-sequence. The ACAS will create a time-sequence movie (mp4) from these images. It will first sort them alpha-numerically. For example, image_000.jpg, image_001.jpg, would be a good naming convention to use.

multiple file in a folder for upload

A well may contain a single image, or it may contain a time-lapse sequence.

Supported file types for single images are .bmp, .jpg, .png, .tif, .tiff.

For many experiments, the well will contain a time sequence of images.

Supported file types for time-lapse sequences are:

a) a collection of single images with the file types .bmp, .jpg, .png, .tif, .tiff. If you supply a collection of single images, be sure that the order of the images corresponds with the time order when the files are sorted alpha-numerically. On a Microsoft operating system, after sorting files by 'name', the files should be in time sequence where time zero is the first file.

b) a movie or multi-frame container such as .mp4, .tif, .tiff, .avi, .mov.

How to Upload a Collection of Frames

Generally, microscope recording systems will output a series of bitmaps or tif files. Tif files can contain a single image or a sequence of images.

upload images or moview

Any of these formats can be uploaded to the well. First determine if your image set is already contained in a single file (for example, mp4, avi, mov, or multi-frame tif). If so you can just directly upload these movie files to the well. Note, only one movie file per well.

If your image sequence is not contained in a movie file, you can also easily upload this sequence of images using the 'multi-image selection' button on the file uploader.

example multi-frame select

Now click "Choose Files". Click on the first file, then hold the shift key and click on the last file in the list, then all files will be selected.

Note: be sure the image file names are alphabetical in time-sequence. The ACAS will create a time-sequence movie (mp4) from these images. It will first sort them alpha-numerically. For example, image_000.jpg, image_001.jpg, would be a good naming convention to use.

multiple file in a folder for upload

Posted on Sep 3, 2018